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Open data
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Basic information
Entry | Database: PDB / ID: 7ylm | ||||||
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Title | Cryo-EM structure of 8-subunit Smc5/6 hinge region | ||||||
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![]() | CELL CYCLE | ||||||
Function / homology | ![]() Smc5-Smc6 complex / SUMO ligase activity / protein sumoylation / chromosome segregation / double-strand break repair via homologous recombination / site of double-strand break / single-stranded DNA binding / damaged DNA binding / ATP hydrolysis activity / zinc ion binding ...Smc5-Smc6 complex / SUMO ligase activity / protein sumoylation / chromosome segregation / double-strand break repair via homologous recombination / site of double-strand break / single-stranded DNA binding / damaged DNA binding / ATP hydrolysis activity / zinc ion binding / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.17 Å | ||||||
![]() | Qian, L. / Jun, Z. / Xiang, Z. / Wang, Z. / Tong, C. / Duo, J. / Zhenguo, C. / Wang, L. | ||||||
Funding support | 1items
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.8 KB | Display | ![]() |
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PDB format | ![]() | 178.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 33914MC ![]() 7ymdC ![]() 7yqhC ![]() 8hqsC ![]() 8i13C ![]() 8i21C ![]() 8i4uC ![]() 8i4vC ![]() 8i4wC ![]() 8i4xC ![]() 8wjlC ![]() 8wjnC ![]() 8wjoC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 126237.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SMC5 / Production host: ![]() ![]() |
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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.) ![]() ![]() Gene: SMC6 / Production host: ![]() ![]() |
#3: Protein | Mass: 30388.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MMS21, GI527_G0001764 / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Cryo-EM structure of 8-subunit Smc5/6 hinge region / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 6.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252457 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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