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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 Pub Date : 2019-12-04 DOI: 10.2210/pdb6ufm/pdb
K. Suddala, J. Zhang
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引用次数: 0
Kiyoshi Nagai (1949–2019) 永井清吉(1949-2019)
IF 16.8 1区 生物学 Pub Date : 2019-12-01 DOI: 10.1016/j.str.2019.11.006
B. Luisi, C. Oubridge
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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 Pub Date : 2019-09-30 DOI: 10.2210/pdb6pj8/pdb
Sangwoo Cho, R. Baker, Ming Ji, S. Urban
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.
细胞膜内的蛋白质切割触发了各种病理生理信号通路,但催化机制尚不清楚。我们在双细胞膜中解决了大肠杆菌菱形蛋白酶的十个结构,经过时间分辨步骤,包括跨膜底物和醛抑制剂上的整个蛋白水解反应。广泛的门打开伴随着底物而不是抑制剂的结合,表明底物和抑制剂走不同的途径到达活性位点。催化出乎意料地开始于细胞外环的运动,并通过活性位点残基的局部贡献引导其通过随后的催化步骤。我们甚至捕捉到了难以捉摸的四面体中间体,它未被切割,但共价连接到催化丝氨酸上,底物被迫在丝氨酸附近急剧弯曲。这种出乎意料的稳定中间体表明,菱形催化使用了前所未有的反应配位,可能涉及对肽键的机械应力,并可能被抑制剂选择性靶向。时间分辨晶体学捕捉了大肠杆菌菱形蛋白酶GlpG在不同催化步骤中的情况,揭示了底物如何到达活性位点和反应中间体。
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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 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
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.
艰难梭菌是一种机会性病原体,当肠道微生物群被抗生素或疾病破坏时,在结肠中形成。艰难梭菌感染(CDI)主要由TcdA和TcdB两种毒力因子引起。在这里,我们报道了一个3.87 a分辨率的TcdB全毒素晶体结构,在内体ph值处捕获了TcdB的独特构象。互补的生物物理学研究表明,TcdB的c端组合重复寡肽(crop)结构域是动态的,可以样品开放和封闭的构象,这可能有助于在中毒期间对环境和细胞信号的响应中调节TcdB的活性。此外,我们报道了三种TcdB-抗体复合物的晶体结构,揭示了抗体如何特异性抑制单个TcdB结构域的活性。我们的研究对TcdB全毒素的结构和功能提供了新的见解,并确定了可用于开发治疗CDI的新疗法和疫苗的内在脆弱性。
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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 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
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.
PIWI相互作用RNA(piRNA)途径部分通过在转座子基因座建立抑制性异染色质来保护基因组完整性。沉默需要piRNA引导的核PIWI蛋白靶向新生转座子转录物,但随后的分子事件尚不清楚。在这里,我们鉴定了SFiNX(沉默因子相互作用的核输出变体),这是果蝇中Piwi介导的共转录沉默所需的一种相互依赖的蛋白质复合物。SFiNX由Nxf2–Nxt1和Piwi相关蛋白Panoramix组成,Nxf2-Nxt1是异二聚体信使RNA输出受体Nxf1–Nxt1的性腺特异性变体。SFiNX突变苍蝇是无菌的,并且表现出转座子去表达,因为负载piRNA的Piwi不能建立异染色质。在SFiNX中,Panoramix招募异染色质效应子,而RNA结合蛋白Nxf2允许共转录沉默。我们的数据揭示了Nxf2可能是如何从RNA转运受体进化为共转录沉默因子的。因此,在后生动物中丰富的NXF变体可以具有不同的分子功能,并且可能被更广泛地用于宿主基因组防御。SFiNX是Nxf2–Nxt1的复合物,是mRNA输出受体Nxf1–Nxt1和Piwi相关蛋白Panoramix的变体,其鉴定表明Nxf2在piRNA引导的共转录转座子沉默中具有RNA输出无关的作用。
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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 Pub Date : 2019-06-26 DOI: 10.2210/PDB6N37/PDB
Q. Cao, D. Boyer, M. Sawaya, P. Ge, D. Eisenberg
The DNA and RNA processing protein TDP-43 undergoes both functional and pathogenic aggregation. Functional TDP-43 aggregates form reversible, transient species such as nuclear bodies, stress granules, and myo-granules. Pathogenic, irreversible TDP-43 aggregates form in amyotrophic lateral sclerosis and other neurodegenerative conditions. Here we find the features of TDP-43 fibrils that confer both reversibility and irreversibility by determining structures of two segments reported to be the pathogenic cores of human TDP-43 aggregation: SegA (residues 311-360), which forms three polymorphs, all with dagger-shaped folds; and SegB A315E (residues 286-331 containing the amyotrophic lateral sclerosis hereditary mutation A315E), which forms R-shaped folds. Energetic analysis suggests that the dagger-shaped polymorphs represent irreversible fibril structures, whereas the SegB polymorph may participate in both reversible and irreversible fibrils. Our structures reveal the polymorphic nature of TDP-43 and suggest how the A315E mutation converts the R-shaped polymorph to an irreversible form that enhances pathology.
DNA和RNA加工蛋白TDP-43经历功能性和致病性聚集。功能性TDP-43聚集体形成可逆的、瞬时的物质,如核体、应力颗粒和肌颗粒。致病性的,不可逆的TDP-43聚集体形成肌萎缩性侧索硬化症和其他神经退行性疾病。在这里,我们通过确定被报道为人类TDP-43聚集的致病核心的两个片段的结构,发现了TDP-43原纤维赋予可逆性和不可逆性的特征:SegA(残基311-360),它形成三个多态,所有具有匕首形折叠;SegB A315E(含有肌萎缩性侧索硬化症遗传突变A315E的残基286-331),形成r形褶皱。能量分析表明,匕首形多态性代表不可逆的原纤维结构,而SegB多态性可能参与可逆和不可逆的原纤维结构。我们的结构揭示了TDP-43的多态性本质,并提示A315E突变如何将r形多态性转化为不可逆的形式,从而增强病理。
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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 Pub Date : 2019-06-26 DOI: 10.2210/pdb6o60/pdb
H. Wang, N. Zheng
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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 Pub Date : 2019-06-24 DOI: 10.2210/PDB6OCG/PDB
Faxiang Li, Yingjie Hu, Shutao Qi, Xuelian Luo, Hongtao Yu
Microtubules are regulated by post-translational modifications of tubulin. The ligation and cleavage of the carboxy-terminal tyrosine of α-tubulin impact microtubule functions during mitosis, cardiomyocyte contraction and neuronal processes. Tubulin tyrosination and detyrosination are mediated by tubulin tyrosine ligase and the recently discovered tubulin detyrosinases, vasohibin 1 and 2 (VASH1 and VASH2) bound to the small vasohibin-binding protein (SVBP). Here, we report the crystal structures of human VASH1-SVBP alone, in complex with a tyrosine-derived covalent inhibitor and bound to the natural product parthenolide. The structures and subsequent mutagenesis analyses explain the requirement for SVBP during tubulin detyrosination, and reveal the basis for the recognition of the C-terminal tyrosine and the acidic α-tubulin tail by VASH1. The VASH1-SVBP-parthenolide structure provides a framework for designing more effective chemical inhibitors of vasohibins, which can be valuable for dissecting their biological functions and may have therapeutic potential.
微管通过微管蛋白的翻译后修饰来调节。α-微管蛋白羧基末端酪氨酸的连接和切割影响微管在有丝分裂、心肌细胞收缩和神经元过程中的功能。微管蛋白酪氨酸化和去酪氨酸化由微管蛋白酪氨酸连接酶和最近发现的与小血管抑制素结合蛋白(SVBP)结合的微管蛋白去酪氨酸酶血管抑制素1和2(VASH1和VASH2)介导。在这里,我们报道了人VASH1-SVBP单独的晶体结构,与酪氨酸衍生的共价抑制剂复合,并与天然产物孤雌内酯结合。结构和随后的诱变分析解释了微管蛋白脱酪氨酸过程中对SVBP的需求,并揭示了VASH1识别C末端酪氨酸和酸性α-微管蛋白尾部的基础。VASH1 SVBP孤雌内酯结构为设计更有效的血管抑制素化学抑制剂提供了一个框架,这对剖析其生物学功能有价值,并可能具有治疗潜力。
{"title":"Crystal structure of VASH1-SVBP complex bound with EpoY","authors":"Faxiang Li, Yingjie Hu, Shutao Qi, Xuelian Luo, Hongtao Yu","doi":"10.2210/PDB6OCG/PDB","DOIUrl":"https://doi.org/10.2210/PDB6OCG/PDB","url":null,"abstract":"Microtubules are regulated by post-translational modifications of tubulin. The ligation and cleavage of the carboxy-terminal tyrosine of α-tubulin impact microtubule functions during mitosis, cardiomyocyte contraction and neuronal processes. Tubulin tyrosination and detyrosination are mediated by tubulin tyrosine ligase and the recently discovered tubulin detyrosinases, vasohibin 1 and 2 (VASH1 and VASH2) bound to the small vasohibin-binding protein (SVBP). Here, we report the crystal structures of human VASH1-SVBP alone, in complex with a tyrosine-derived covalent inhibitor and bound to the natural product parthenolide. The structures and subsequent mutagenesis analyses explain the requirement for SVBP during tubulin detyrosination, and reveal the basis for the recognition of the C-terminal tyrosine and the acidic α-tubulin tail by VASH1. The VASH1-SVBP-parthenolide structure provides a framework for designing more effective chemical inhibitors of vasohibins, which can be valuable for dissecting their biological functions and may have therapeutic potential.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"26 1","pages":"583-591"},"PeriodicalIF":16.8,"publicationDate":"2019-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46002638","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
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 Pub Date : 2019-06-24 DOI: 10.2210/PDB6NUH/PDB
Petria S. Thompson, K. M. Amidon, Kareem N. Mohni, D. Cortez, B. Eichman
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.
碱基(AP)位点是阻断复制聚合酶的最常见的DNA损伤之一。5-羟甲基胞嘧啶结合,胚胎干细胞特异性蛋白(HMCES)在单链DNA (ssDNA)的背景下识别和处理这些病变。一种HMCES dna -蛋白交联(DPC)中间体被认为可以保护AP位点免受核酸内切酶和易出错聚合酶的攻击。HMCES的高度进化保守的sos反应相关肽酶(SRAP)结构域及其大肠杆菌同源YedK介导病变识别。本文从YedK DPC的晶体结构中揭示了SRAP结构域保护AP位点的基础。YedK在开环的AP位点与其氨基端半胱氨酸残基的α-氨基和巯基取代基之间形成稳定的噻唑烷键。噻唑烷键解释了HMCES DPC的显著稳定性,其抗链切割和蛋白水解要求的分辨率。此外,其结构表明,HMCES对复制聚合酶遇到AP病变时发现的ssDNA连接处的AP位点具有特异性。
{"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 Pub Date : 2019-06-24 DOI: 10.2210/PDB6OB6/PDB
Nicholas Wright, Seok-Yong Lee
The human equilibrative nucleoside transporter 1 (hENT1), a member of the SLC29 family, plays crucial roles in adenosine signaling, cellular uptake of nucleoside for DNA and RNA synthesis, and nucleoside-derived anticancer and antiviral drug transport in humans. Because of its central role in adenosine signaling, it is the target of adenosine reuptake inhibitors (AdoRI), several of which are used clinically. Despite its importance in human physiology and pharmacology, the molecular basis of hENT1-mediated adenosine transport and its inhibition by AdoRIs are limited, owing to the absence of structural information on hENT1. Here, we present crystal structures of hENT1 in complex with two chemically distinct AdoRIs: dilazep and S-(4-nitrobenzyl)-6-thioinosine (NBMPR). Combined with mutagenesis study, our structural analyses elucidate two distinct inhibitory mechanisms exhibited on hENT1 and provide insight into adenosine recognition and transport. Our studies provide a platform for improved pharmacological intervention of adenosine and nucleoside analog drug transport by hENT1.
人平衡核苷转运蛋白1(hENT1)是SLC29家族的一员,在腺苷信号传导、用于DNA和RNA合成的核苷的细胞摄取以及核苷衍生的人类抗癌和抗病毒药物转运中发挥着至关重要的作用。由于其在腺苷信号传导中的核心作用,它是腺苷再摄取抑制剂(AdoRI)的靶点,其中几种在临床上使用。尽管hENT1在人类生理学和药理学中很重要,但由于缺乏hENT1的结构信息,hENT1介导的腺苷转运及其被AdoRIs抑制的分子基础是有限的。在这里,我们展示了hENT1与两种化学上不同的AdoRIs的复合物的晶体结构:地西泮和S-(4-硝基苄基)-6-硫肌苷(NBMPR)。结合诱变研究,我们的结构分析阐明了对hENT1表现出的两种不同的抑制机制,并为腺苷的识别和转运提供了见解。我们的研究为hENT1改善腺苷和核苷类似物药物转运的药理学干预提供了一个平台。
{"title":"Human equilibrative nucleoside transporter-1, S-(4-nitrobenzyl)-6-thioinosine bound, merohedrally twinned","authors":"Nicholas Wright, Seok-Yong Lee","doi":"10.2210/PDB6OB6/PDB","DOIUrl":"https://doi.org/10.2210/PDB6OB6/PDB","url":null,"abstract":"The human equilibrative nucleoside transporter 1 (hENT1), a member of the SLC29 family, plays crucial roles in adenosine signaling, cellular uptake of nucleoside for DNA and RNA synthesis, and nucleoside-derived anticancer and antiviral drug transport in humans. Because of its central role in adenosine signaling, it is the target of adenosine reuptake inhibitors (AdoRI), several of which are used clinically. Despite its importance in human physiology and pharmacology, the molecular basis of hENT1-mediated adenosine transport and its inhibition by AdoRIs are limited, owing to the absence of structural information on hENT1. Here, we present crystal structures of hENT1 in complex with two chemically distinct AdoRIs: dilazep and S-(4-nitrobenzyl)-6-thioinosine (NBMPR). Combined with mutagenesis study, our structural analyses elucidate two distinct inhibitory mechanisms exhibited on hENT1 and provide insight into adenosine recognition and transport. Our studies provide a platform for improved pharmacological intervention of adenosine and nucleoside analog drug transport by hENT1.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"26 1","pages":"599-606"},"PeriodicalIF":16.8,"publicationDate":"2019-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44664546","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: 1
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Nature Structural &Molecular Biology
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