+Open data
-Basic information
Entry | Database: PDB / ID: 7yqh | ||||||
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Title | Cryo-EM structure of 8-subunit Smc5/6 | ||||||
Components |
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Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information Smc5-Smc6 complex / resolution of DNA recombination intermediates / chromosome separation / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / ATPase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / chromosome separation / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / ATPase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / protein serine/threonine kinase inhibitor activity / SUMO transferase activity / postreplication repair / recombinational repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / nuclear envelope / single-stranded DNA binding / site of double-strand break / DNA recombination / damaged DNA binding / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / mitochondrion / zinc ion binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å | ||||||
Authors | Qian, L. / Jun, Z. / Xiang, Z. / Tong, C. / Zhaoning, W. / Duo, J. / Zhenguo, C. / Lanfeng, W. | ||||||
Funding support | 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Cryo-EM structures of Smc5/6 in multiple states reveal its assembly and functional mechanisms. Authors: Qian Li / Jun Zhang / Cory Haluska / Xiang Zhang / Lei Wang / Guangfeng Liu / Zhaoning Wang / Duo Jin / Tong Cheng / Hongxia Wang / Yuan Tian / Xiangxi Wang / Lei Sun / Xiaolan Zhao / ...Authors: Qian Li / Jun Zhang / Cory Haluska / Xiang Zhang / Lei Wang / Guangfeng Liu / Zhaoning Wang / Duo Jin / Tong Cheng / Hongxia Wang / Yuan Tian / Xiangxi Wang / Lei Sun / Xiaolan Zhao / Zhenguo Chen / Lanfeng Wang / Abstract: Smc5/6 is a member of the eukaryotic structural maintenance of chromosomes (SMC) family of complexes with important roles in genome maintenance and viral restriction. However, limited structural ...Smc5/6 is a member of the eukaryotic structural maintenance of chromosomes (SMC) family of complexes with important roles in genome maintenance and viral restriction. However, limited structural understanding of Smc5/6 hinders the elucidation of its diverse functions. Here, we report cryo-EM structures of the budding yeast Smc5/6 complex in eight-subunit, six-subunit and five-subunit states. Structural maps throughout the entire length of these complexes reveal modularity and key elements in complex assembly. We show that the non-SMC element (Nse)2 subunit supports the overall shape of the complex and uses a wedge motif to aid the stability and function of the complex. The Nse6 subunit features a flexible hook region for attachment to the Smc5 and Smc6 arm regions, contributing to the DNA repair roles of the complex. Our results also suggest a structural basis for the opposite effects of the Nse1-3-4 and Nse5-6 subcomplexes in regulating Smc5/6 ATPase activity. Collectively, our integrated structural and functional data provide a framework for understanding Smc5/6 assembly and function. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yqh.cif.gz | 756.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yqh.ent.gz | 609.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yqh_validation.pdf.gz | 833.5 KB | Display | wwPDB validaton report |
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Full document | 7yqh_full_validation.pdf.gz | 902.1 KB | Display | |
Data in XML | 7yqh_validation.xml.gz | 116.1 KB | Display | |
Data in CIF | 7yqh_validation.cif.gz | 175.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/7yqh ftp://data.pdbj.org/pub/pdb/validation_reports/yq/7yqh | HTTPS FTP |
-Related structure data
Related structure data | 34025MC 7ylmC 7ymdC 8hqsC 8i13C 8i21C 8i4uC 8i4vC 8i4wC 8i4xC 8wjlC 8wjnC 8wjoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 126237.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: SMC5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08204 |
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#2: Protein | Mass: 128199.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: SMC6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12749 |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 30388.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: NSE2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P38632, Transferases; Acyltransferases; Aminoacyltransferases |
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#4: Protein | Mass: 53836.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: KRE29 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P40026 |
-Non-structural maintenance of chromosome element ... , 2 types, 2 molecules EG
#5: Protein | Mass: 64079.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: NSE5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03718 |
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#7: Protein | Mass: 34005.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: NSE3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q05541 |
-Non-structural maintenance of chromosomes element ... , 2 types, 2 molecules FH
#6: Protein | Mass: 38373.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: NSE1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q07913, RING-type E3 ubiquitin transferase |
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#8: Protein | Mass: 46195.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: NSE4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6L0Z6W9 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of 8-subunit Smc5/6 / Type: COMPLEX / Entity ID: #1-#5, #8, #6-#7 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1056147 / Symmetry type: POINT | ||||||||||||||||||||||||
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