protein_name
stringlengths
4
4
structure_title
stringlengths
3
322
main_text
stringlengths
0
302k
3NAO
A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit Cell
A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit Tong Wang1, Ruojie Sha1, Jens Birktoft1, Jianping Zheng1, Chengde Mao2, and Nadrian C. Seeman* 1 Department of Chemistry, New York University, New York, New York 10003 2 Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907 Abstrac...
3NAR
Crystal structure of ZHX1 HD4 (zinc-fingers and homeoboxes protein 1, homeodomain 4)
Bird et al. BMC Structural Biology 2010, 10:13 http://www.biomedcentral.com/1472-6807/10/13 Open Access RESEARCH ARTICLE © 2010 Bird et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons At- tribution License (http://creativecommons.org/licenses/by/2.0), ...
3NAU
Crystal structure of ZHX2 HD2 (zinc-fingers and homeoboxes protein 2, homeodomain 2)
Bird et al. BMC Structural Biology 2010, 10:13 http://www.biomedcentral.com/1472-6807/10/13 Open Access RESEARCH ARTICLE © 2010 Bird et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons At- tribution License (http://creativecommons.org/licenses/by/2.0), ...
3NAW
Crystal structure of E. coli O157:H7 effector protein NleL
Biochemical and Structural Studies of a HECT-like Ubiquitin Ligase from Escherichia coli O157:H7* Received for publication,July 23, 2010, and in revised form, September 28, 2010 Published, JBC Papers in Press,October 27, 2010, DOI 10.1074/jbc.M110.167643 David Yin-wei Lin‡, Jianbo Diao§, Daoguo Zhou‡, and Jue Chen‡¶1 F...
3NAX
PDK1 in complex with inhibitor MP7
Genetic and Pharmacological Inhibition of PDK1 in Cancer Cells CHARACTERIZATION OF A SELECTIVE ALLOSTERIC KINASE INHIBITOR □ S Received for publication,June 20, 2010, and in revised form, November 15, 2010 Published, JBC Papers in Press,November 30, 2010, DOI 10.1074/jbc.M110.156463 Kumiko Nagashima‡1, Stuart D. Shumwa...
3NAZ
Basal state form of Yeast Glycogen Synthase
Structural basis for glucose-6-phosphate activation of glycogen synthase Sulochanadevi Baskaran, Peter J. Roach, Anna A. DePaoli-Roach, and Thomas D. Hurley1 Department of Biochemistry and Molelcular Biology, Indiana University School of Medicine, Indianapolis, IN 46202-5122 Edited by Gregory A. Petsko, Brandeis Univer...
3NB0
Glucose-6-Phosphate activated form of Yeast Glycogen Synthase
Structural basis for glucose-6-phosphate activation of glycogen synthase Sulochanadevi Baskaran, Peter J. Roach, Anna A. DePaoli-Roach, and Thomas D. Hurley1 Department of Biochemistry and Molelcular Biology, Indiana University School of Medicine, Indianapolis, IN 46202-5122 Edited by Gregory A. Petsko, Brandeis Univer...
3NB2
Crystal structure of E. coli O157:H7 effector protein NleL
Biochemical and Structural Studies of a HECT-like Ubiquitin Ligase from Escherichia coli O157:H7* Received for publication,July 23, 2010, and in revised form, September 28, 2010 Published, JBC Papers in Press,October 27, 2010, DOI 10.1074/jbc.M110.167643 David Yin-wei Lin‡, Jianbo Diao§, Daoguo Zhou‡, and Jue Chen‡¶1 F...
3NB3
The host outer membrane proteins OmpA and OmpC are packed at specific sites in the Shigella phage Sf6 virion as structural components
The host outer membrane proteins OmpA and OmpC are associated with the Shigella phage Sf6 virion Haiyan Zhao‡, Reuben D. Sequeira‡, Nadezhda A. Galeva†, and Liang Tang‡,* Haiyan Zhao: zhaohy@ku.edu; Reuben D. Sequeira: sequen@ku.edu; Nadezhda A. Galeva: galeva@ku.edu ‡ Department of Molecular Biosciences, University of...
3NB6
Crystal structure of Aquifex aeolicus peptidoglycan glycosyltransferase in complex with Methylphosphoryl Neryl Moenomycin
Functional and Structural Analysis of a Key Region of the Cell Wall Inhibitor Moenomycin Shinichiro Fuse†, Hirokazu Tsukamoto†, Yanqiu Yuan‡, Tsung-Shing Andrew Wang†, Yi Zhang†, Megan Bolla†, Suzanne Walker‡,*, Piotr Sliz#, and Daniel Kahne†,§,* † Department of Chemistry and Chemical Biology, Harvard University, Cambr...
3NB7
Crystal structure of Aquifex Aeolicus Peptidoglycan Glycosyltransferase in complex with Decarboxylated Neryl Moenomycin
Functional and Structural Analysis of a Key Region of the Cell Wall Inhibitor Moenomycin Shinichiro Fuse†, Hirokazu Tsukamoto†, Yanqiu Yuan‡, Tsung-Shing Andrew Wang†, Yi Zhang†, Megan Bolla†, Suzanne Walker‡,*, Piotr Sliz#, and Daniel Kahne†,§,* † Department of Chemistry and Chemical Biology, Harvard University, Cambr...
3NB8
Crystal structure of oxidized H88Q Synechocystis sp. PCYA
Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants†,# Amanda C. Kohler§,∥, David D. Gae±, Michael A. Richley‡, Stefan Stoll§, Alexander Gunn§, Sunghyuk Lim§, Shelley S. Martin‡, Tzanko I. Doukov#, R. David Britt§, James B. Ames, J. Clark Lagarias‡, and Andrew J. Fisher§,‡,* §Dep...
3NB9
Crystal structure of radical H88Q Synechocystis sp. PCYA
Structural basis for hydration dynamics in radical stabilization of bilin reductase mutants†,# Amanda C. Kohler§,∥, David D. Gae±, Michael A. Richley‡, Stefan Stoll§, Alexander Gunn§, Sunghyuk Lim§, Shelley S. Martin‡, Tzanko I. Doukov#, R. David Britt§, James B. Ames, J. Clark Lagarias‡, and Andrew J. Fisher§,‡,* §Dep...
3NBB
Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from hansenula polymorpha
Mutation at a Strictly-Conserved, Active-Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity† Zhi-wei Chen*, Saumen Datta*,#, Jennifer L. DuBois‡,§, Judith P. Klinman‡,¶, and F. Scott Mathews*,¶ *Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine...
3NBC
Clitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 4.4
Bivalent Carbohydrate Binding Is Required for Biological Activity of Clitocybe nebularis Lectin (CNL), the N,N-Diacetyllactosediamine (GalNAc1–4GlcNAc, LacdiNAc)-specific Lectin from Basidiomycete C. nebularis*□ S Received for publication,October 25, 2011, and in revised form January 17, 2012 Published, JBC Papers in...
3NBD
Clitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 7.1
Bivalent Carbohydrate Binding Is Required for Biological Activity of Clitocybe nebularis Lectin (CNL), the N,N-Diacetyllactosediamine (GalNAc1–4GlcNAc, LacdiNAc)-specific Lectin from Basidiomycete C. nebularis*□ S Received for publication,October 25, 2011, and in revised form January 17, 2012 Published, JBC Papers in...
3NBE
Clitocybe nebularis ricin B-like lectin (CNL) in complex with N,N'-diacetyllactosediamine
Bivalent Carbohydrate Binding Is Required for Biological Activity of Clitocybe nebularis Lectin (CNL), the N,N-Diacetyllactosediamine (GalNAc1–4GlcNAc, LacdiNAc)-specific Lectin from Basidiomycete C. nebularis*□ S Received for publication,October 25, 2011, and in revised form January 17, 2012 Published, JBC Papers in...
3NBH
Crystal structure of human RMI1C-RMI2 complex
Crystal Structures of RMI1 and RMI2, Two OB-fold Regulatory Subunits of the BLM Complex Feng Wang1,2, Yuting Yang1,2, Thiyam Ramsing Singh3, Valeria Busygina4, Rong Guo5, Ke Wan1,2, Weidong Wang5, Patrick Sung4, Amom Ruhikanta Meetei3, and Ming Lei1,2 1Howard Hughes Medical Institute, University of Michigan Medical S...
3NBI
Crystal structure of human RMI1 N-terminus
Crystal Structures of RMI1 and RMI2, Two OB-fold Regulatory Subunits of the BLM Complex Feng Wang1,2, Yuting Yang1,2, Thiyam Ramsing Singh3, Valeria Busygina4, Rong Guo5, Ke Wan1,2, Weidong Wang5, Patrick Sung4, Amom Ruhikanta Meetei3, and Ming Lei1,2 1Howard Hughes Medical Institute, University of Michigan Medical S...
3NBJ
Crystal Structure of Y305F mutant of the copper amine oxidase from Hansenula polymorpha expressed in yeast
Mutation at a Strictly-Conserved, Active-Site Tyrosine in the Copper Amine Oxidase Leads to Uncontrolled Oxygenase Activity† Zhi-wei Chen*, Saumen Datta*,#, Jennifer L. DuBois‡,§, Judith P. Klinman‡,¶, and F. Scott Mathews*,¶ *Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine...
3NBN
Crystal structure of a dimer of Notch Transcription Complex trimers on HES1 DNA
Structural and Mechanistic Insights into Cooperative Assembly of Dimeric Notch Transcription Complexes Kelly L. Arnett1,2, Matthew Hass3, Debbie G. McArthur1,2, Ma. Xenia G. Ilagan3, Jon C. Aster2, Raphael Kopan3, and Stephen C. Blacklow1,2,4 1Department of Cancer Biology, Dana Farber Cancer Institute, Boston MA 02115 ...
3NBQ
Human uridine phosphorylase 1 (hUPP1) with 5-fluorouracil
Active Site Conformational Dynamics in Human Uridine Phosphorylase 1 Tarmo P. Roosild*, Samantha Castronovo Department of Drug Development, Nevada Cancer Institute, Las Vegas, Nevada, United States of America Abstract Uridine phosphorylase (UPP) is a central enzyme in the pyrimidine salvage pathway, catalyzing the reve...
3NBS
Crystal structure of dimeric cytochrome c from horse heart
Cytochrome c polymerization by successive domain swapping at the C-terminal helix Shun Hirotaa,1, Yoko Hattoria, Satoshi Nagaoa, Midori Taketab, Hirofumi Komorib,c, Hironari Kamikuboa, Zhonghua Wanga,d, Isao Takahashia, Shigeru Negie, Yukio Sugiurae, Mikio Kataokaa, and Yoshiki Higuchib,c aGraduate School of Materials ...
3NBT
Crystal structure of trimeric cytochrome c from horse heart
Cytochrome c polymerization by successive domain swapping at the C-terminal helix Shun Hirotaa,1, Yoko Hattoria, Satoshi Nagaoa, Midori Taketab, Hirofumi Komorib,c, Hironari Kamikuboa, Zhonghua Wanga,d, Isao Takahashia, Shigeru Negie, Yukio Sugiurae, Mikio Kataokaa, and Yoshiki Higuchib,c aGraduate School of Materials ...
3NBU
Crystal structure of pGI glucosephosphate isomerase
Macro-to-Micro Structural Proteomics: Native Source Proteins for High-Throughput Crystallization Monica Totir1.¤a, Nathaniel Echols1.¤b, Max Nanao2, Christine L. Gee1¤c, Alisa Moskaleva1¤d, Scott Gradia3, Anthony T. Iavarone3, James M. Berger1, Andrew P. May4, Chloe Zubieta1*¤e, Tom Alber1* 1 Department of Molecular an...
3NBX
Crystal structure of E. coli RavA (Regulatory ATPase variant A) in complex with ADP
Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity Majida El Bakkouria, Irina Gutscheb, Usheer Kanjeea, Boyu Zhaoa, Miao Yua, Gael Goretc, Guy Schoehnb,c, Wim P. Burmeisterb,d, and Walid A. Hourya,1 aDepartment of Biochemistry, Un...
3NCB
A mutant human Prolactin receptor antagonist H180A in complex with the extracellular domain of the human prolactin receptor
Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical for pH-dependent Receptor Recognition and Activation*□ S Received for publication,August 4, 2010, and in revised form, September 8, 2010 Published, JBC Papers in Press,September 30, 2010, DOI 10.1074/jbc.M110.172072 Mandar V. Kulka...
3NCC
A human Prolactin receptor antagonist in complex with the mutant extracellular domain H188A of the human prolactin receptor
Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical for pH-dependent Receptor Recognition and Activation*□ S Received for publication,August 4, 2010, and in revised form, September 8, 2010 Published, JBC Papers in Press,September 30, 2010, DOI 10.1074/jbc.M110.172072 Mandar V. Kulka...
3NCE
A mutant human Prolactin receptor antagonist H27A in complex with the mutant extracellular domain H188A of the human prolactin receptor
Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical for pH-dependent Receptor Recognition and Activation*□ S Received for publication,August 4, 2010, and in revised form, September 8, 2010 Published, JBC Papers in Press,September 30, 2010, DOI 10.1074/jbc.M110.172072 Mandar V. Kulka...
3NCF
A mutant human Prolactin receptor antagonist H30A in complex with the mutant extracellular domain H188A of the human prolactin receptor
Two Independent Histidines, One in Human Prolactin and One in Its Receptor, Are Critical for pH-dependent Receptor Recognition and Activation*□ S Received for publication,August 4, 2010, and in revised form, September 8, 2010 Published, JBC Papers in Press,September 30, 2010, DOI 10.1074/jbc.M110.172072 Mandar V. Kulka...
3NCG
Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with bumped kinase inhibitor NM-PP1
Published on Web Date: July 07, 2010 r 2010 American Chemical Society 331 DOI: 10.1021/ml100096t |ACS Med. Chem. Lett. 2010, 1, 331–335 pubs.acs.org/acsmedchemlett Discovery of Potent and Selective Inhibitors of CDPK1 from C. parvum and T. gondii Ryan C. Murphy,†,O Kayode K. Ojo,‡,O Eric T. Larson,§, ) Alejandro Castel...
3NCH
Yeast Glycogen Synthase (Gsy2p) Basal State Conformation
Structural basis for glucose-6-phosphate activation of glycogen synthase Sulochanadevi Baskaran, Peter J. Roach, Anna A. DePaoli-Roach, and Thomas D. Hurley1 Department of Biochemistry and Molelcular Biology, Indiana University School of Medicine, Indianapolis, IN 46202-5122 Edited by Gregory A. Petsko, Brandeis Univer...
3NCI
RB69 DNA Polymerase Ternary Complex with dCTP Opposite dG at 1.8 angstrom resolution
pubs.acs.org/biochemistry Published on Web 12/15/2010 r 2010 American Chemical Society Biochemistry 2011, 50, 581–590 581 DOI: 10.1021/bi101192f Insights into Base Selectivity from the 1.8 A˚ Resolution Structure of an RB69 DNA Polymerase Ternary Complex† Mina Wang,‡ Shuangluo Xia,‡ Gregor Blaha,‡ Thomas A. Steitz,‡,§,...
3NCL
Crystal Structure of MT-SP1 bound to Benzamidine Phosphonate Inhibitor
Peptide length and prime-side sterics influence potency of peptide phosphonate protease inhibitors Christopher M. Brown*,1, Manisha Ray*,1, Aura A. Eroy-Reveles2, Pascal Egea3,§, Cheryl Tajon4, and Charles S. Craik2,# 1Graduate Group in Biochemistry and Molecular Biology, University of California, San Francisco, CA 2De...
3NCT
X-ray crystal structure of the bacterial conjugation factor PsiB, a negative regulator of reca
X-ray Crystal Structure of the Bacterial Conjugation Factor PsiB, a Negative Regulator of RecA* Received for publication,June 7, 2010 Published, JBC Papers in Press,July 21, 2010, DOI 10.1074/jbc.M110.152298 Vessela Petrova‡, Kenneth A. Satyshur§, Nicholas P. George§, Darrell McCaslin¶, Michael M. Cox‡¶, and James L. K...
3NCU
Structural and functional insights into pattern recognition by the innate immune receptor RIG-I
Structural and functional insights into pattern recognition by the innate immune receptor RIG-I Yanli Wang1,5, Janos Ludwig2,5, Christine Schuberth2, Marion Goldeck2, Martin Schlee2, Haitao Li1, Stefan Juranek3, Gang Sheng1, Ronald Micura4, Thomas Tuschl3, Gunther Hartmann2, and Dinshaw J. Patel1 1Structural Biology...
3NCV
NgoL
The C-Terminal Domain of the MutL Homolog from Neisseria gonorrhoeae Forms an Inverted Homodimer Sivakumar Namadurai1., Deepti Jain1., Dhananjay S. Kulkarni2., Chaitanya R. Tabib2, Peter Friedhoff3, Desirazu N. Rao2, Deepak T. Nair1* 1 Laboratory 4, National Centre for Biological Sciences, Bangalore, India, 2 Departmen...
3NCW
Crystal structure of EHEC O157:H7 intimin
Crystal Structure of EHEC Intimin: Insights into the Complementarity between EPEC and EHEC Yong Yi1,3,5., Ying Ma1,2., Feng Gao6., Xuhu Mao1., Hao Peng2,5, Youjun Feng2,4,5, Zheng Fan2,5, Guihua Wang2,4,5, Gang Guo1, Jinghua Yan2,5, Hao Zeng1, Quanming Zou1*, George F. Gao2,5,7* 1 Department of Clinical Microbiology an...
3NCX
Crystal structure of EHEC O157:H7 intimin mutant
Crystal Structure of EHEC Intimin: Insights into the Complementarity between EPEC and EHEC Yong Yi1,3,5., Ying Ma1,2., Feng Gao6., Xuhu Mao1., Hao Peng2,5, Youjun Feng2,4,5, Zheng Fan2,5, Guihua Wang2,4,5, Gang Guo1, Jinghua Yan2,5, Hao Zeng1, Quanming Zou1*, George F. Gao2,5,7* 1 Department of Clinical Microbiology an...
3NCY
X-ray crystal structure of an arginine agmatine antiporter (AdiC) in complex with a Fab fragment
Structure of a Prokaryotic Virtual Proton Pump at 3.2 Å Resolution Yiling Fang, Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454 Hariharan Jayaram, Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02...
3ND0
X-ray crystal structure of a slow cyanobacterial Cl-/H+ antiporter
Structure of a slow CLC Cl−/H+ antiporter from a cyanobacterium Hariharan Jayaram, Janice L. Robertson, Fang Wu, Carole Williams, and Christopher Miller Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02454 Abstract X-ray crystal structures have been previously d...
3ND3
Uhelix 16-mer dsRNA
The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate BLAINE H.M. MOOERS1 and AMRITANSHU SINGH Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, BRC 466, Oklahoma City, Oklahoma 73104-5419, USA ABSTRACT Guide RNAs bind antiparallel t...
3ND4
Watson-Crick 16-mer dsRNA
The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate BLAINE H.M. MOOERS1 and AMRITANSHU SINGH Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, BRC 466, Oklahoma City, Oklahoma 73104-5419, USA ABSTRACT Guide RNAs bind antiparallel t...
3ND5
Crystal structure of phosphopantetheine adenylyltransferase (PPAT) from Enterococcus faecalis
Mol. Cells 32, 431-435, November 30, 2011 DOI/10.1007/s10059-011-0102-y Crystal Structure of Phosphopantetheine Adenylyltransferase from Enterococcus faecalis in the Ligand-Unbound State and in Complex with ATP and Pantetheine Hye-Jin Yoon1, Ji Yong Kang1, Bunzo Mikami2, Hyung Ho Lee3,4,*...
3ND6
Crystal structure of phosphopantetheine adenylyltransferase (PPAT) in complex with ATP from Enterococcus faecalis
Mol. Cells 32, 431-435, November 30, 2011 DOI/10.1007/s10059-011-0102-y Crystal Structure of Phosphopantetheine Adenylyltransferase from Enterococcus faecalis in the Ligand-Unbound State and in Complex with ATP and Pantetheine Hye-Jin Yoon1, Ji Yong Kang1, Bunzo Mikami2, Hyung Ho Lee3,4,*...
3ND7
Crystal structure of phosphopantetheine adenylyltransferase from Enterococcus faecalis in the ligand-unbound state and in complex with ATP and pantetheine
Mol. Cells 32, 431-435, November 30, 2011 DOI/10.1007/s10059-011-0102-y Crystal Structure of Phosphopantetheine Adenylyltransferase from Enterococcus faecalis in the Ligand-Unbound State and in Complex with ATP and Pantetheine Hye-Jin Yoon1, Ji Yong Kang1, Bunzo Mikami2, Hyung Ho Lee3,4,*...
3NDD
Cleaved antitrypsin with P10 Pro, and P9-P6 Asp
Loop-Sheet Mechanism of Serpin Polymerization Tested by Reactive Center Loop Mutations*□ S Received for publication,June 18, 2010 Published, JBC Papers in Press,July 28, 2010, DOI 10.1074/jbc.M110.156042 Masayuki Yamasaki, Timothy J. Sendall, Laura E. Harris, Giles M. W. Lewis, and James A. Huntington1 From the Departm...
3NDF
Cleaved antitrypsin with P8-P6 Asp
Loop-Sheet Mechanism of Serpin Polymerization Tested by Reactive Center Loop Mutations*□ S Received for publication,June 18, 2010 Published, JBC Papers in Press,July 28, 2010, DOI 10.1074/jbc.M110.156042 Masayuki Yamasaki, Timothy J. Sendall, Laura E. Harris, Giles M. W. Lewis, and James A. Huntington1 From the Departm...
3NDH
Restriction endonuclease in complex with substrate DNA
DNA intercalation without flipping in the specific ThaI–DNA complex Malgorzata Firczuk1,2, Marek Wojciechowski1,3, Honorata Czapinska1,3 and Matthias Bochtler1,3,4,* 1International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland, 2Department of Immunology, Centre of Biostructure Research, Med...
3NDK
RB69 DNA Polymerase (Y567A) Ternary Complex with dCTP Opposite dG
Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures Shuangluo Xia1,¥, Mina Wang1,¥, Harold R. Lee1,*, Arjun Sinha1,Δ, Gregor Blaha2, Thomas Christian1, Jimin Wang2,Ω,†, and William Konigsberg1,Ω,† 1 Department of Molecular Biop...
3NDN
Crystal structure of O-succinylhomoserine sulfhydrylase from Mycobacterium tuberculosis covalently bound to pyridoxal-5-phosphate
Increasing the Structural Coverage of Tuberculosis Drug Targets Loren Baugha,b, Isabelle Phana,b, Darren W. Begleya,c, Matthew C. Cliftona,c, Brianna Armoura,c, David M. Dranowa,c, Brandy M. Taylora,c, Marvin M. Muruthia,c, Jan Abendrotha,c, James W. Fairmanc, David Fox IIIc, Shellie H. Dieterichc, Bart L. Stakera,b,...
3NDO
Crystal structure of deoxyribose phosphate aldolase from mycobacterium smegmatis
Increasing the Structural Coverage of Tuberculosis Drug Targets Loren Baugha,b, Isabelle Phana,b, Darren W. Begleya,c, Matthew C. Cliftona,c, Brianna Armoura,c, David M. Dranowa,c, Brandy M. Taylora,c, Marvin M. Muruthia,c, Jan Abendrotha,c, James W. Fairmanc, David Fox IIIc, Shellie H. Dieterichc, Bart L. Stakera,b,...
3NE1
Mycobacterium tuberculosis Acyl Carrier Protein Synthase in complex with sulfate ion
research papers Acta Cryst. (2011). D67, 657–669 doi:10.1107/S0907444911020221 657 Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations Kuppan Gokulan,a Anup Aggarwal,a Lance Shipman...
3NE3
Mycobacterium tuberculosis Acyl Carrier Protein Synthase Apo structure
research papers Acta Cryst. (2011). D67, 657–669 doi:10.1107/S0907444911020221 657 Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations Kuppan Gokulan,a Anup Aggarwal,a Lance Shipman...
3NE4
1.8 Angstrom structure of intact native wild-type alpha-1-antitrypsin
structural communications 1492 doi:10.1107/S1744309111040267 Acta Cryst. (2011). F67, 1492–1497 Acta Crystallographica Section F Structural Biology and Crystallization Communications ISSN 1744-3091 Therapeutic target-site variability in a1-antitrypsin characterized at high resolution Anathe O. M. Patschull,a Lakshmi Se...
3NE5
Crystal structure of the CusBA heavy-metal efflux complex from Escherichia coli
Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli Chih-Chia Su1,ψ, Feng Long1,ψ, Michael T. Zimmermann2, Kanagalaghatta R. Rajashankar3, Robert L. Jernigan2,4, and Edward W. Yu1,2,4,5,* 1Department of Chemistry, Iowa State University, Ames, IA 50011, USA 2Bioinformatics and Computational Bio...
3NE6
RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Opposite dG
Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures Shuangluo Xia1,¥, Mina Wang1,¥, Harold R. Lee1,*, Arjun Sinha1,Δ, Gregor Blaha2, Thomas Christian1, Jimin Wang2,Ω,†, and William Konigsberg1,Ω,† 1 Department of Molecular Biop...
3NE7
Crystal structure of paia n-acetyltransferase from thermoplasma acidophilum in complex with coenzyme a
Crystal structure of the novel PaiA N-acetyltransferase from Thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production E.V. Filippova1,2, L. Shuvalova1,2, G. Minasov1,2, O. Kiryukhina1,2, Y. Zhang3, S. Clancy2, I. Radhakrishnan3, A. Joachimiak2, and W.F. Anderson1,2,★ 1D...
3NE8
The crystal structure of a domain from N-acetylmuramoyl-l-alanine amidase of Bartonella henselae str. Houston-1
A conformational switch controls cell wall remodeling enzymes required for bacterial cell division Desirée C. Yang1, Kemin Tan2, Andrzej Joachimiak2, and Thomas G. Bernhardt*,1 1Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115 2Biosciences Division, Argonne National Laboratory, Arg...
3NE9
Chronobacterium ammoiniagenes apo-ACPS structure
research papers Acta Cryst. (2011). D67, 657–669 doi:10.1107/S0907444911020221 657 Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations Kuppan Gokulan,a Anup Aggarwal,a Lance Shipman...
3NEA
Crystal Structure of Peptidyl-tRNA hydrolase from Francisella tularensis
structural communications 446 doi:10.1107/S174430911100515X Acta Cryst. (2011). F67, 446–449 Acta Crystallographica Section F Structural Biology and Crystallization Communications ISSN 1744-3091 Structure of Francisella tularensis peptidyl-tRNA hydrolase Teresa E. Clarke,a,b Vladimir Romanov,a,b Robert Lam,a,b Scott A....
3NEC
Crystal Structure of Toxoplasma gondii Profilin
Structure-Based Analysis of Toxoplasma gondii Profilin: A Parasite-Specific Motif is Required for Recognition by Toll-like Receptor 11 Kaury Kuceraa, A. Alicia Koblanskyb, Lauren P. Saundersa, Kendra B. Fredericka, Enrique M. De La Cruza, Sankar Ghoshb, and Yorgo Modisa,* aDepartment of Molecular Biophysics & Biochemis...
3NED
mRouge
Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries Roberto A. Chicaa,1, Matthew M. Mooreb, Benjamin D. Allenb, and Stephen L. Mayoa,b,2 aDivision of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125; and bDivision of C...
3NEF
High-resolution pyrabactin-bound PYL1 structure
Functional Mechanism of the Abscisic Acid Agonist Pyrabactin*□ S Received for publication,May 27, 2010, and in revised form, June 6, 2010 Published, JBC Papers in Press,June 16, 2010, DOI 10.1074/jbc.M110.149005 Qi Hao‡§1, Ping Yin‡§1, Chuangye Yan‡¶1, Xiaoqiu Yuan‡§, Wenqi Li‡§, Zhiping Zhang, Lei Liu, Jiawei Wang‡¶...
3NEG
Pyrabactin-bound PYL1 structure in the open and close forms
Functional Mechanism of the Abscisic Acid Agonist Pyrabactin*□ S Received for publication,May 27, 2010, and in revised form, June 6, 2010 Published, JBC Papers in Press,June 16, 2010, DOI 10.1074/jbc.M110.149005 Qi Hao‡§1, Ping Yin‡§1, Chuangye Yan‡¶1, Xiaoqiu Yuan‡§, Wenqi Li‡§, Zhiping Zhang, Lei Liu, Jiawei Wang‡¶...
3NEK
Crystal structure of a nitrogen repressor-like protein MJ0159 from Methanococcus jannaschii
Structural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR Goragot Wisedchaisri1,*, David M. Dranow1,*, Thomas J. Lie2, Jeffrey B. Bonanno3, Yury Patskovsky3, Sinem A. Ozyurt4, J. Michael Sauder4, Steven C. Almo3, Stephen R. Wasserman5, Stephen K. Burley4, John A...
3NEL
Aspartyl-tRNA synthetase complexed with aspartic acid
The EMBO Journal Vol.17 No.17 pp.5227–5237, 1998 Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation E.Schmitt1,2, L.Moulinier1, S.Fujiwara3, T.Imanaka4, J.-C.Thierry1 and D.Moras1,5 1Laboratoire de Biologie Structurale, Ins...
3NEM
Aspartyl-tRNA synthetase complexed with aspartyl adenylate
The EMBO Journal Vol.17 No.17 pp.5227–5237, 1998 Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation E.Schmitt1,2, L.Moulinier1, S.Fujiwara3, T.Imanaka4, J.-C.Thierry1 and D.Moras1,5 1Laboratoire de Biologie Structurale, Ins...
3NEN
Unliganded aspartyl-tRNA synthetase from thermococcus kodakarensis
The EMBO Journal Vol.17 No.17 pp.5227–5237, 1998 Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation E.Schmitt1,2, L.Moulinier1, S.Fujiwara3, T.Imanaka4, J.-C.Thierry1 and D.Moras1,5 1Laboratoire de Biologie Structurale, Ins...
3NEQ
Crystal structure of the chimeric muscarinic toxin MT7 with loop 3 from MT1
Engineering of Three-Finger Fold Toxins Creates Ligands with Original Pharmacological Profiles for Muscarinic and Adrenergic Receptors Carole Fruchart-Gaillard1., Gilles Mourier1., Guillaume Blanchet1,2, Laura Vera1, Nicolas Gilles1, Rene´e Me´nez1, Elodie Marcon1, Enrico A. Stura1, Denis Servent1* 1 CEA, iBiTecS, Serv...
3NER
Structure of Human Type B Cytochrome b5
Accommodating a Non-Conservative Internal Mutation by Water- Mediated Hydrogen-Bonding Between β-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome b5 Sudharsan Parthasarathy1, Adriana Altuve2, Simon Terzyan3, Xuejun Zhang3, Krzysztof Kuczera1,2, Mario Rivera2, and David R. Benson1,2,* 1D...
3NEZ
mRojoA
Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries Roberto A. Chicaa,1, Matthew M. Mooreb, Benjamin D. Allenb, and Stephen L. Mayoa,b,2 aDivision of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125; and bDivision of C...
3NF2
Crystal structure of polyprenyl synthetase from Streptomyces coelicolor A3(2)
Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily Frank H. Wallrappa,b, Jian-Jung Panc, Gurusankar Ramamoorthyc, Daniel E. Almonacidb,d, Brandan S. Hilleriche, Ronald Seidele, Yury Patskovskye, Patricia C. Babbittb,d, Steven C. Almoe, Matthew P. Jacobsona,b,1, and C. ...
3NF3
Crystal structure of BoNT/A LC with JTH-NB-7239 peptide
Iterative Structure-Based Peptide-Like Inhibitor Design against the Botulinum Neurotoxin Serotype A Jorge E. Zuniga1, Jared T. Hammill2, Omri Drory1, Jonathan E. Nuss3, James C. Burnett4, Rick Gussio5, Peter Wipf2*, Sina Bavari3, Axel T. Brunger1* 1 Howard Hughes Medical Institute and Departments of Molecular and Cellu...
3NF4
Crystal structure of acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to flavin adenine dinucleotide
Increasing the Structural Coverage of Tuberculosis Drug Targets Loren Baugha,b, Isabelle Phana,b, Darren W. Begleya,c, Matthew C. Cliftona,c, Brianna Armoura,c, David M. Dranowa,c, Brandy M. Taylora,c, Marvin M. Muruthia,c, Jan Abendrotha,c, James W. Fairmanc, David Fox IIIc, Shellie H. Dieterichc, Bart L. Stakera,b,...
3NF5
Crystal structure of the C-terminal domain of nuclear pore complex component NUP116 from Candida glabrata
Atomic Structure of the Nuclear Pore Complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata Parthasarathy Sampathkumar1,2,*, Seung Joong Kim3,4,5, Danalyn Manglicmot2, Kevin T. Bain2, Jeremiah Gilmore2, Tarun Gheyi2, Jeremy Phillips3,4,5,6, Ursula Pieper3,4,5, Javier Fernandez-Martinez7, Josef ...
3NFD
Chronobacterium ammoniagenes ACPS-CoA complex
research papers Acta Cryst. (2011). D67, 657–669 doi:10.1107/S0907444911020221 657 Acta Crystallographica Section D Biological Crystallography ISSN 0907-4449 Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations Kuppan Gokulan,a Anup Aggarwal,a Lance Shipman...
3NFE
The crystal structure of hemoglobin I from trematomus newnesi in deoxygenated state
An Order-Disorder Transition Plays a Role in Switching Off the Root Effect in Fish Hemoglobins*□ S Received for publication,May 11, 2010, and in revised form, June 17, 2010 Published, JBC Papers in Press,July 7, 2010, DOI 10.1074/jbc.M110.143537 Alessandro Vergara‡§, Luigi Vitagliano§, Antonello Merlino‡§, Filomena Sic...
3NFQ
Crystal structure of the conserved central domain of yeast Spn1/Iws1
The transcription factor Spn1 regulates gene expression via a highly conserved novel structural motif Venugopal Pujari1, Catherine A. Radebaugh2, Jayanth V. Chodaparambil3, Uma M. Muthurajan2, Adam R. Almeida2, Julie A. Fischbeck2, Karolin Luger2, and Laurie A. Stargell2,* 2 Department of Biochemistry and Molecular Bio...
3NFT
Near-atomic resolution analysis of BipD- A component of the type-III secretion system of Burkholderia pseudomallei
structural communications 990 doi:10.1107/S1744309110026333 Acta Cryst. (2010). F66, 990–993 Acta Crystallographica Section F Structural Biology and Crystallization Communications ISSN 1744-3091 Near-atomic resolution analysis of BipD, a component of the type III secretion system of Burkholderia pseudomallei M. Pal,a,b...
3NFW
Crystal structure of nitrilotriacetate monooxygenase component B (A0R521 homolog) from Mycobacterium thermoresistibile
structural communications 1100 doi:10.1107/S1744309111012541 Acta Cryst. (2011). F67, 1100–1105 Acta Crystallographica Section F Structural Biology and Crystallization Communications ISSN 1744-3091 Structure of nitrilotriacetate monooxygenase component B from Mycobacterium thermoresistibile Y. Zhang,a,b* T. E. Edwards,...
3NFY
The Structure of Human Bisphosphoglycerate Mutase to 1.94A
structural communications Acta Cryst. (2010). F66, 1415–1420 doi:10.1107/S1744309110035475 1415 Acta Crystallographica Section F Structural Biology and Crystallization Communications ISSN 1744-3091 Unliganded structure of human bisphosphoglycerate mutase reveals side-chain movements induced by ligand binding A. Patters...
3NFZ
Crystal structure of murine aminoacylase 3 in complex with N-acetyl-L-tyrosine
Structures of aminoacylase 3 in complex with acetylated substrates Jennifer M. Hsieha,b,1, Kirill Tsirulnikovc,1, Michael R. Sawayad, Nathaniel Magilnickc, Natalia Abuladzec, Ira Kurtzc, Jeff Abramsonb,2, and Alexander Pushkinc,2 aDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095...
3NG2
Crystal structure of the RNF4 ring domain dimer
RING DOMAIN DIMERIZATION IS ESSENTIAL FOR RNF4 FUNCTION Chu Wai Liew*,†, Huaiyu Sun‡,†, Tony Hunter‡, and Catherine L. Day*,1 *Biochemistry Department, University of Otago, Dunedin 9054, New Zealand. ‡Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, ...
3NG3
Crystal structure of deoxyribose phosphate aldolase from mycobacterium avium 104 in a schiff base with an unknown aldehyde
Increasing the Structural Coverage of Tuberculosis Drug Targets Loren Baugha,b, Isabelle Phana,b, Darren W. Begleya,c, Matthew C. Cliftona,c, Brianna Armoura,c, David M. Dranowa,c, Brandy M. Taylora,c, Marvin M. Muruthia,c, Jan Abendrotha,c, James W. Fairmanc, David Fox IIIc, Shellie H. Dieterichc, Bart L. Stakera,b,...
3NG4
Ternary complex of peptidoglycan recognition protein (PGRP-S) with Maltose and N-Acetylglucosamine at 1.7 A Resolution
Multiligand Specificity of Pathogen-associated Molecular Pattern-binding Site in Peptidoglycan Recognition Protein*□ S Received for publication,May 24, 2011, and in revised form, June 13, 2011 Published, JBC Papers in Press,July 22, 2011, DOI 10.1074/jbc.M111.264374 Pradeep Sharma‡, Divya Dube‡, Mau Sinha‡, Biswajit Mi...
3NG6
The crystal structure of hemoglobin I from Trematomus newnesi in deoxygenated state obtained through an oxidation/reduction cycle in which potassium hexacyanoferrate and sodium dithionite were alternatively added
An Order-Disorder Transition Plays a Role in Switching Off the Root Effect in Fish Hemoglobins*□ S Received for publication,May 11, 2010, and in revised form, June 17, 2010 Published, JBC Papers in Press,July 7, 2010, DOI 10.1074/jbc.M110.143537 Alessandro Vergara‡§, Luigi Vitagliano§, Antonello Merlino‡§, Filomena Sic...
3NG7
Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity
Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family Galina Kachalovaa, Karl Deckerb, Andrew Holtc, and Hans D. Bartunika,1 aMax Planck Unit for Structural Molecular Biology, Notkestrasse 85, 22607 Hamburg, Germany; bInstitut für Bio...
3NGB
Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120
Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01 Tongqing Zhou1, Ivelin Georgiev1,*, Xueling Wu1,*, Zhi-Yong Yang1,*, Kaifan Dai1, Andrés Finzi2, Young Do Kwon1, Johannes Scheid3, Wei Shi1, Ling Xu1, Yongping Yang1, Jiang Zhu1, Michel C. Nussenzweig3, Joseph Sodroski2,4, Lawrence Shapi...
3NGD
Structural Basis for Proficient Incorporation of dTTP Opposite O6-methylguanine by Human DNA Polymerase Iota
Structural Basis for Proficient Incorporation of dTTP Opposite O6-Methylguanine by Human DNA Polymerase *□ S Received for publication,September 9, 2010 Published, JBC Papers in Press,October 20, 2010, DOI 10.1074/jbc.M110.183665 Matthew G. Pence‡, Jeong-Yun Choi§, Martin Egli‡, and F. Peter Guengerich‡§1 From the ‡Dep...
3NGG
X-ray Structure of Omwaprin
Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography James R. Banigan,1,2 Kalyaneswar Mandal,1,2,3 Michael R. Sawaya,4,5 Vilasak Thammavongsa,6 Antoni P. A. Hendrickx,6,7 Olaf Schneewind,6 Todd O. Yeates,4,5,8 and Stephen B. H. Kent1,2,...
3NGH
Molecular Analysis of the Interaction of the HDL Receptor SR-BI with the Adaptor Protein PDZK1
In Vitro and in Vivo Analysis of the Binding of the C Terminus of the HDL Receptor Scavenger Receptor Class B, Type I (SR-BI), to the PDZ1 Domain of Its Adaptor Protein PDZK1* Received for publication,July 14, 2010, and in revised form, August 13, 2010 Published, JBC Papers in Press,August 25, 2010, DOI 10.1074/jbc.M11...
3NGI
RB69 DNA Polymerase (Y567A) Ternary Complex with dTTP Opposite dG
Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures Shuangluo Xia1,¥, Mina Wang1,¥, Harold R. Lee1,*, Arjun Sinha1,Δ, Gregor Blaha2, Thomas Christian1, Jimin Wang2,Ω,†, and William Konigsberg1,Ω,† 1 Department of Molecular Biop...
3NGK
PduA from Salmonella enterica Typhimurium
Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell*□ S Received for publication,July 1, 2010, and in revised form, September 19, 2010 Published, JBC Papers in Press,September 24, 2010, DOI 10.1074/jbc.M110.160580 Christopher S. Crowley‡, Duilio Cascio¶, Michael...
3NGM
Crystal structure of lipase from Gibberella zeae
RESEARCH ARTICLE Crystal structure of a secreted lipase from Gibberella zeae reveals a novel “double-lock” mechanism Zhiyong Lou1, Ming Li2, Yuna Sun3, Ye Liu2, Zheng Liu2, Wenping Wu2, Zihe Rao1,3✉ 1 Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China 2 Novozymes China, 14 Xinxi Lu, Shangdi Zo...
3NGN
Crystal structure of the human CNOT6L nuclease domain in complex with AMP
Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity Hui Wang1,2, Masahiro Morita3, Xiuna Yang2, Toru Suzuki3, Wen Yang1, Jiao Wang1, Kentaro Ito3, Quan Wang1, Cong Zhao2, Mark Bartlam1,*, Tadashi Yamamoto3,* and Zihe Rao1,2 1Tianjin Key Laboratory of Protein Science, Colleg...
3NGO
Crystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA
Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity Hui Wang1,2, Masahiro Morita3, Xiuna Yang2, Toru Suzuki3, Wen Yang1, Jiao Wang1, Kentaro Ito3, Quan Wang1, Cong Zhao2, Mark Bartlam1,*, Tadashi Yamamoto3,* and Zihe Rao1,2 1Tianjin Key Laboratory of Protein Science, Colleg...
3NGP
High resolution structure of alpha-spectrin SH3 domain mutant with a redesigned core
structural communications Acta Cryst. (2010). F66, 1023–1027 doi:10.1107/S1744309110030095 1023 Acta Crystallographica Section F Structural Biology and Crystallization Communications ISSN 1744-3091 High-resolution structure of an a-spectrin SH3-domain mutant with a redesigned hydrophobic core Ana Ca´mara-Artigas,a* Mon...
3NGQ
Crystal structure of the human CNOT6L nuclease domain
Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity Hui Wang1,2, Masahiro Morita3, Xiuna Yang2, Toru Suzuki3, Wen Yang1, Jiao Wang1, Kentaro Ito3, Quan Wang1, Cong Zhao2, Mark Bartlam1,*, Tadashi Yamamoto3,* and Zihe Rao1,2 1Tianjin Key Laboratory of Protein Science, Colleg...
3NGV
Crystal structure of AnSt-D7L1
The Function and Three-Dimensional Structure of a Thromboxane A2/Cysteinyl Leukotriene-Binding Protein from the Saliva of a Mosquito Vector of the Malaria Parasite Patricia H. Alvarenga1,2, Ivo M. B. Francischetti1, Eric Calvo1, Anderson Sa´-Nunes1,3, Jose´ M. C. Ribeiro1, John F. Andersen1* 1 Laboratory of Malaria and...