Nature Structural &Molecular Biology最新文献_第2页

Cocrystal Structure of the Nocardia farcinica ileS T-box riboswitch in complex with its cognate tRNA 法氏诺卡氏菌ileS-T-box核糖开关与其同源tRNA复合物的共晶结构

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-12-04 DOI: 10.2210/pdb6ufm/pdb

K. Suddala, J. Zhang

引用次数: 0

Kiyoshi Nagai (1949–2019) 永井清吉（1949-2019）

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-12-01 DOI: 10.1016/j.str.2019.11.006

B. Luisi, C. Oubridge

引用次数: 1

Time-resolved structural snapshot of proteolysis by GlpG inside the membrane 膜内GlpG蛋白水解的时间分辨结构快照

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-09-30 DOI: 10.2210/pdb6pj8/pdb

Sangwoo Cho, R. Baker, Ming Ji, S. Urban

{"title":"Time-resolved structural snapshot of proteolysis by GlpG inside the membrane","authors":"Sangwoo Cho, R. Baker, Ming Ji, S. Urban","doi":"10.2210/pdb6pj8/pdb","DOIUrl":"https://doi.org/10.2210/pdb6pj8/pdb","url":null,"abstract":"Protein cleavage inside the cell membrane triggers various pathophysiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing time-resolved steps that encompass the entire proteolytic reaction on a transmembrane substrate and an aldehyde inhibitor. Extensive gate opening accompanied substrate, but not inhibitor, binding, revealing that substrates and inhibitors take different paths to the active site. Catalysis unexpectedly commenced with, and was guided through subsequent catalytic steps by, motions of an extracellular loop, with local contributions from active site residues. We even captured the elusive tetrahedral intermediate that is uncleaved but covalently attached to the catalytic serine, about which the substrate was forced to bend dramatically. This unexpectedly stable intermediate indicates rhomboid catalysis uses an unprecedented reaction coordinate that may involve mechanically stressing the peptide bond, and could be selectively targeted by inhibitors. Time-resolved crystallography captures Escherichia coli rhomboid protease GlpG in different steps of catalysis, revealing how substrate reaches the active site and reaction intermediates.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"26 1","pages":"910-918"},"PeriodicalIF":16.8,"publicationDate":"2019-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46100269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

Structure of the pore forming fragment of Clostridium difficile toxin B in complex with VHH 5D 艰难梭菌毒素B与VHH 5D复合物成孔片段的结构

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-07-10 DOI: 10.2210/PDB6OQ6/PDB

Peng Chen, K. Lam, Zheng Liu, Frank A. Mindlin, Baohua Chen, Craig B. Gutierrez, Lan Huang, Yongrong Zhang, Therwa Hamza, H. Feng, T. Matsui, M. Bowen, K. Perry, Rongsheng Jin

{"title":"Structure of the pore forming fragment of Clostridium difficile toxin B in complex with VHH 5D","authors":"Peng Chen, K. Lam, Zheng Liu, Frank A. Mindlin, Baohua Chen, Craig B. Gutierrez, Lan Huang, Yongrong Zhang, Therwa Hamza, H. Feng, T. Matsui, M. Bowen, K. Perry, Rongsheng Jin","doi":"10.2210/PDB6OQ6/PDB","DOIUrl":"https://doi.org/10.2210/PDB6OQ6/PDB","url":null,"abstract":"Clostridium difficile is an opportunistic pathogen that establishes in the colon when the gut microbiota are disrupted by antibiotics or disease. C. difficile infection (CDI) is largely caused by two virulence factors, TcdA and TcdB. Here, we report a 3.87-A-resolution crystal structure of TcdB holotoxin that captures a unique conformation of TcdB at endosomal pH. Complementary biophysical studies suggest that the C-terminal combined repetitive oligopeptides (CROPs) domain of TcdB is dynamic and can sample open and closed conformations that may facilitate modulation of TcdB activity in response to environmental and cellular cues during intoxication. Furthermore, we report three crystal structures of TcdB-antibody complexes that reveal how antibodies could specifically inhibit the activities of individual TcdB domains. Our studies provide novel insight into the structure and function of TcdB holotoxin and identify intrinsic vulnerabilities that could be exploited to develop new therapeutics and vaccines for the treatment of CDI.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"26 1","pages":"712-719"},"PeriodicalIF":16.8,"publicationDate":"2019-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46209076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Crystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15 与Nxt1/p15复合物中dmNxf2-NTF2样结构域的晶体结构

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-07-03 DOI: 10.2210/PDB6MRK/PDB

Júlia Batki, J. Schnabl, Juncheng Wang, Dominik Handler, Veselin I. Andreev, Christian E. Stieger, M. Novatchkova, Lisa Lampersberger, Kotryna Kauneckaitė, W. Xie, K. Mechtler, D. Patel, J. Brennecke

{"title":"Crystal structure of dmNxf2 NTF2-like domain in complex with Nxt1/p15","authors":"Júlia Batki, J. Schnabl, Juncheng Wang, Dominik Handler, Veselin I. Andreev, Christian E. Stieger, M. Novatchkova, Lisa Lampersberger, Kotryna Kauneckaitė, W. Xie, K. Mechtler, D. Patel, J. Brennecke","doi":"10.2210/PDB6MRK/PDB","DOIUrl":"https://doi.org/10.2210/PDB6MRK/PDB","url":null,"abstract":"The PIWI-interacting RNA (piRNA) pathway protects genome integrity in part through establishing repressive heterochromatin at transposon loci. Silencing requires piRNA-guided targeting of nuclear PIWI proteins to nascent transposon transcripts, yet the subsequent molecular events are not understood. Here, we identify SFiNX (silencing factor interacting nuclear export variant), an interdependent protein complex required for Piwi-mediated cotranscriptional silencing in Drosophila. SFiNX consists of Nxf2–Nxt1, a gonad-specific variant of the heterodimeric messenger RNA export receptor Nxf1–Nxt1 and the Piwi-associated protein Panoramix. SFiNX mutant flies are sterile and exhibit transposon derepression because piRNA-loaded Piwi is unable to establish heterochromatin. Within SFiNX, Panoramix recruits heterochromatin effectors, while the RNA binding protein Nxf2 licenses cotranscriptional silencing. Our data reveal how Nxf2 might have evolved from an RNA transport receptor into a cotranscriptional silencing factor. Thus, NXF variants, which are abundant in metazoans, can have diverse molecular functions and might have been coopted for host genome defense more broadly. Identification of SFiNX, a complex of Nxf2–Nxt1, a variant of the mRNA export receptor Nxf1–Nxt1 and the Piwi-associated protein Panoramix, demonstrates an RNA export independent role for Nxf2 in piRNA-guided cotranscriptional transposon silencing.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"26 1","pages":"720-731"},"PeriodicalIF":16.8,"publicationDate":"2019-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47062235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

SegA-sym, conformation of TDP-43 low complexity domain segment A sym SegA-sym, TDP-43低复杂度域段A系统的构象

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-06-26 DOI: 10.2210/PDB6N37/PDB

Q. Cao, D. Boyer, M. Sawaya, P. Ge, D. Eisenberg

引用次数: 8

Crystal structure of GGTase3-FBXL2-SKP1 complex GGTase3-FBXL2-SKP1配合物的晶体结构

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-06-26 DOI: 10.2210/pdb6o60/pdb

H. Wang, N. Zheng

引用次数: 0

Crystal structure of VASH1-SVBP complex bound with EpoY 与EpoY结合的VASH1-SVBP复合物的晶体结构

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-06-24 DOI: 10.2210/PDB6OCG/PDB

Faxiang Li, Yingjie Hu, Shutao Qi, Xuelian Luo, Hongtao Yu

引用次数: 2

Non-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site analog 大肠杆菌YedK和含有基本位点类似物的ssDNA之间的非共价dna -蛋白复合物

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-06-24 DOI: 10.2210/PDB6NUH/PDB

Petria S. Thompson, K. M. Amidon, Kareem N. Mohni, D. Cortez, B. Eichman

{"title":"Non-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site analog","authors":"Petria S. Thompson, K. M. Amidon, Kareem N. Mohni, D. Cortez, B. Eichman","doi":"10.2210/PDB6NUH/PDB","DOIUrl":"https://doi.org/10.2210/PDB6NUH/PDB","url":null,"abstract":"Abasic (AP) sites are one of the most common DNA lesions that block replicative polymerases. 5-hydroxymethylcytosine binding, embryonic stem cell-specific protein (HMCES) recognizes and processes these lesions in the context of single-stranded DNA (ssDNA). A HMCES DNA-protein cross-link (DPC) intermediate is thought to shield the AP site from endonucleases and error-prone polymerases. The highly evolutionarily conserved SOS-response associated peptidase (SRAP) domain of HMCES and its Escherichia coli ortholog YedK mediate lesion recognition. Here we uncover the basis of AP site protection by SRAP domains from a crystal structure of the YedK DPC. YedK forms a stable thiazolidine linkage between a ring-opened AP site and the α-amino and sulfhydryl substituents of its amino-terminal cysteine residue. The thiazolidine linkage explains the remarkable stability of the HMCES DPC, its resistance to strand cleavage and the proteolysis requirement for resolution. Furthermore, its structure reveals that HMCES has specificity for AP sites in ssDNA at junctions found when replicative polymerases encounter the AP lesion.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"26 1","pages":"613-618"},"PeriodicalIF":16.8,"publicationDate":"2019-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42837871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Human equilibrative nucleoside transporter-1, S-(4-nitrobenzyl)-6-thioinosine bound, merohedrally twinned 人平衡核苷转运体- 1,5 -(4-硝基苄基)-6-硫代氨基糖苷结合，双侧孪生

IF 16.8 1区生物学

Nature Structural &Molecular Biology Pub Date : 2019-06-24 DOI: 10.2210/PDB6OB6/PDB

Nicholas Wright, Seok-Yong Lee

引用次数: 1