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III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae III2-IV2酿酒酵母线粒体呼吸超复合体
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-12-26 DOI: 10.2210/pdb6hu9/pdb
Andrew M. Hartley, N. Lukoyanova, Yunyi Zhang, Alfredo Cabrera-Orefice, S. Arnold, B. Meunier, N. Pinotsis, A. Maréchal
{"title":"III2-IV2 mitochondrial respiratory supercomplex from S. cerevisiae","authors":"Andrew M. Hartley, N. Lukoyanova, Yunyi Zhang, Alfredo Cabrera-Orefice, S. Arnold, B. Meunier, N. Pinotsis, A. Maréchal","doi":"10.2210/pdb6hu9/pdb","DOIUrl":"https://doi.org/10.2210/pdb6hu9/pdb","url":null,"abstract":"Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc1 (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a III2IV2 SC at 3.3 A resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A—involved in allosteric inhibition by ATP—may arise from its association with CIII. The CIII–CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":" ","pages":""},"PeriodicalIF":16.8,"publicationDate":"2018-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45447636","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
Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore 出芽酵母着丝点CBF3-core-Ndc10-DBD复合物的低温电镜结构
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-11-26 DOI: 10.2210/PDB6GYP/PDB
K. Yan, Ziguo Zhang, Jing Yang, S. McLaughlin, D. Barford
{"title":"Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore","authors":"K. Yan, Ziguo Zhang, Jing Yang, S. McLaughlin, D. Barford","doi":"10.2210/PDB6GYP/PDB","DOIUrl":"https://doi.org/10.2210/PDB6GYP/PDB","url":null,"abstract":"Kinetochores are multicomponent complexes responsible for coordinating the attachment of centromeric DNA to mitotic-spindle microtubules. The point centromeres of budding yeast are organized into three centromeric determining elements (CDEs), and are associated with the centromere-specific nucleosome Cse4. Deposition of Cse4 at CEN loci is dependent on the CBF3 complex that engages CDEIII to direct Cse4 nucleosomes to CDEII. To understand how CBF3 recognizes CDEIII and positions Cse4, we determined a cryo-EM structure of a CBF3-CEN complex. CBF3 interacts with CEN DNA as a head-to-head dimer that includes the whole of CDEIII and immediate 3' regions. Specific CEN-binding of CBF3 is mediated by a Cep3 subunit of one of the CBF3 protomers that forms major groove interactions with the conserved and essential CCG and TGT motifs of CDEIII. We propose a model for a CBF3-Cse4-CEN complex with implications for understanding CBF3-directed deposition of the Cse4 nucleosome at CEN loci.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"25 1","pages":"1103-1110"},"PeriodicalIF":16.8,"publicationDate":"2018-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47952677","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 a functional obligate respiratory supercomplex from Mycobacterium smegmatis 耻垢分枝杆菌功能性专性呼吸超复合体的结构
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-11-07 DOI: 10.2210/pdb6hwh/pdb
B. Wiseman, R. Nitharwal, O. Fedotovskaya, Jacob Schäfer, Hui Guo, Qie Kuang, S. Benlekbir, D. Sjöstrand, Pia Ädelroth, J. Rubinstein, P. Brzezinski, M. Högbom
{"title":"Structure of a functional obligate respiratory supercomplex from Mycobacterium smegmatis","authors":"B. Wiseman, R. Nitharwal, O. Fedotovskaya, Jacob Schäfer, Hui Guo, Qie Kuang, S. Benlekbir, D. Sjöstrand, Pia Ädelroth, J. Rubinstein, P. Brzezinski, M. Högbom","doi":"10.2210/pdb6hwh/pdb","DOIUrl":"https://doi.org/10.2210/pdb6hwh/pdb","url":null,"abstract":"","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"25 1","pages":"1128-1136"},"PeriodicalIF":16.8,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43068937","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
Solution NMR structure of a de novo designed double-stranded beta-helix 溶液核磁共振结构的一个从头设计的双链β -螺旋
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-11-07 DOI: 10.2210/pdb6e5c/pdb
E. Marcos, T. M. Chidyausiku, A. McShan, T. Evangelidis, S. Nerli, N. Sgourakis, K. Tripsianes, D. Baker
{"title":"Solution NMR structure of a de novo designed double-stranded beta-helix","authors":"E. Marcos, T. M. Chidyausiku, A. McShan, T. Evangelidis, S. Nerli, N. Sgourakis, K. Tripsianes, D. Baker","doi":"10.2210/pdb6e5c/pdb","DOIUrl":"https://doi.org/10.2210/pdb6e5c/pdb","url":null,"abstract":"","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"1 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2018-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68198532","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: 34
Human sigma-1 receptor bound to (+)-pentazocine 人sigma-1受体与(+)-戊唑嗪结合
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-10-17 DOI: 10.2210/PDB6DK1/PDB
H. Schmidt, Robin M. Betz, R. Dror, A. Kruse
{"title":"Human sigma-1 receptor bound to (+)-pentazocine","authors":"H. Schmidt, Robin M. Betz, R. Dror, A. Kruse","doi":"10.2210/PDB6DK1/PDB","DOIUrl":"https://doi.org/10.2210/PDB6DK1/PDB","url":null,"abstract":"","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"25 1","pages":"981-987"},"PeriodicalIF":16.8,"publicationDate":"2018-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48599379","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: 19
Complex of APLF factor and Ku heterodimer bound to DNA APLF因子和Ku异二聚体与DNA结合的复合体
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-10-05 DOI: 10.2210/PDB6ERF/PDB
C. Nemoz, V. Ropars, P. Frit, A. Gontier, P. Drevet, J. Yu, R. Guérois, A. Pitois, A. Comte, C. Delteil, N. Barboule, Pierre Legrand, S. Baconnais, Y. Yin, S. Tadi, E. Barbet-Massin, I. Berger, E. Cam, M. Modesti, E. Rothenberg, P. Calsou, J. Charbonnier
{"title":"Complex of APLF factor and Ku heterodimer bound to DNA","authors":"C. Nemoz, V. Ropars, P. Frit, A. Gontier, P. Drevet, J. Yu, R. Guérois, A. Pitois, A. Comte, C. Delteil, N. Barboule, Pierre Legrand, S. Baconnais, Y. Yin, S. Tadi, E. Barbet-Massin, I. Berger, E. Cam, M. Modesti, E. Rothenberg, P. Calsou, J. Charbonnier","doi":"10.2210/PDB6ERF/PDB","DOIUrl":"https://doi.org/10.2210/PDB6ERF/PDB","url":null,"abstract":"The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBM motifs bind remote sites of the Ku80 α/β domain. The X-KBM occupies an internal pocket formed by an unprecedented large outward rotation of the Ku80 α/β domain. We observe independent recruitment of the APLF-interacting protein XRCC4 and of XLF to laser-irradiated sites via binding of A- and X-KBMs, respectively, to Ku80. Finally, we show that mutation of the X-KBM and A-KBM binding sites in Ku80 compromises both the efficiency and accuracy of end joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchor points to build the intricate interaction network required for NHEJ.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"25 1","pages":"971-980"},"PeriodicalIF":16.8,"publicationDate":"2018-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43524372","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: 14
Structure of atOSCA3.1 channel atOSCA3.1通道的结构
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-09-06 DOI: 10.2210/PDB5Z1F/PDB
Mingfeng Zhang, Dali Wang, Yunlu Kang, Jing-Xiang Wu, Fuqiang Yao, Chengfang Pan, Zhiqiang Yan, Chen Song, Lei Chen
{"title":"Structure of atOSCA3.1 channel","authors":"Mingfeng Zhang, Dali Wang, Yunlu Kang, Jing-Xiang Wu, Fuqiang Yao, Chengfang Pan, Zhiqiang Yan, Chen Song, Lei Chen","doi":"10.2210/PDB5Z1F/PDB","DOIUrl":"https://doi.org/10.2210/PDB5Z1F/PDB","url":null,"abstract":"Mechanosensitive ion channels convert mechanical stimuli into a flow of ions. These channels are widely distributed from bacteria to higher plants and humans, and are involved in many crucial physiological processes. Here we show that two members of the OSCA protein family in Arabidopsis thaliana, namely AtOSCA1.1 and AtOSCA3.1, belong to a new class of mechanosensitive ion channels. We solve the structure of the AtOSCA1.1 channel at 3.5-A resolution and AtOSCA3.1 at 4.8-A resolution by cryo-electron microscopy. OSCA channels are symmetric dimers that are mediated by cytosolic inter-subunit interactions. Strikingly, they have structural similarity to the mammalian TMEM16 family proteins. Our structural analysis accompanied with electrophysiological studies identifies the ion permeation pathway within each subunit and suggests a conformational change model for activation.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"25 1","pages":"850-858"},"PeriodicalIF":16.8,"publicationDate":"2018-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49209488","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: 13
Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor 5-HT2B受体激活和偏向性激动的结构决定因素
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-08-29 DOI: 10.2210/PDB6DRX/PDB
J. McCorvy, Daniel Wacker, Sheng Wang, B. Agegnehu, Jing Liu, Katherine Lansu, A. Tribo, Reid H. J. Olsen, T. Che, Jian Jin, B. Roth
{"title":"Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor","authors":"J. McCorvy, Daniel Wacker, Sheng Wang, B. Agegnehu, Jing Liu, Katherine Lansu, A. Tribo, Reid H. J. Olsen, T. Che, Jian Jin, B. Roth","doi":"10.2210/PDB6DRX/PDB","DOIUrl":"https://doi.org/10.2210/PDB6DRX/PDB","url":null,"abstract":"","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"25 1","pages":"787-796"},"PeriodicalIF":16.8,"publicationDate":"2018-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49588851","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: 85
Cryo-EM structure of mouse TRPV3 in complex with 2-Aminoethoxydiphenyl borate (2-APB) 小鼠TRPV3与2-氨基乙氧基二苯硼酸酯(2-APB)配合物的低温电镜结构
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-08-20 DOI: 10.2210/PDB6DVY/PDB
A. Singh, L. L. McGoldrick, A. Sobolevsky
{"title":"Cryo-EM structure of mouse TRPV3 in complex with 2-Aminoethoxydiphenyl borate (2-APB)","authors":"A. Singh, L. L. McGoldrick, A. Sobolevsky","doi":"10.2210/PDB6DVY/PDB","DOIUrl":"https://doi.org/10.2210/PDB6DVY/PDB","url":null,"abstract":"Transient receptor potential vanilloid subfamily member 3 (TRPV3) channel plays a crucial role in skin physiology and pathophysiology. Mutations in TRPV3 are associated with various skin diseases, including Olmsted syndrome, atopic dermatitis, and rosacea. Here we present the cryo-electron microscopy structures of full-length mouse TRPV3 in the closed apo and agonist-bound open states. The agonist binds three allosteric sites distal to the pore. Channel opening is accompanied by conformational changes in both the outer pore and the intracellular gate. The gate is formed by the pore-lining S6 helices that undergo local α-to-π helical transitions, elongate, rotate, and splay apart in the open state. In the closed state, the shorter S6 segments are entirely α-helical, expose their nonpolar surfaces to the pore, and hydrophobically seal the ion permeation pathway. These findings further illuminate TRP channel activation and can aid in the design of drugs for the treatment of inflammatory skin conditions, itch, and pain.","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"25 1","pages":"805-813"},"PeriodicalIF":16.8,"publicationDate":"2018-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45165464","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: 26
Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68 整合素-v -8与fab - 8B8和68的复合物
IF 16.8 1区 生物学
Nature Structural &Molecular Biology Pub Date : 2018-07-25 DOI: 10.2210/pdb6djp/pdb
A. Cormier, M. Campbell, S. Nishimura, Y. Cheng
{"title":"Integrin alpha-v beta-8 in complex with the Fabs 8B8 and 68","authors":"A. Cormier, M. Campbell, S. Nishimura, Y. Cheng","doi":"10.2210/pdb6djp/pdb","DOIUrl":"https://doi.org/10.2210/pdb6djp/pdb","url":null,"abstract":"","PeriodicalId":18836,"journal":{"name":"Nature Structural &Molecular Biology","volume":"1 1","pages":""},"PeriodicalIF":16.8,"publicationDate":"2018-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68198040","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: 16
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