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- PDB-7yqh: Cryo-EM structure of 8-subunit Smc5/6 -

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Entry
Database: PDB / ID: 7yqh
TitleCryo-EM structure of 8-subunit Smc5/6
Components
  • (Non-structural maintenance of chromosome element ...) x 2
  • (Non-structural maintenance of chromosomes element ...) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
  • DNA repair protein KRE29
  • E3 SUMO-protein ligase MMS21
KeywordsCELL CYCLE
Function / homology
Function and homology information


Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / chromosome separation / 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 / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / chromosome separation / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / ATPase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / DNA damage tolerance / recombinational repair / regulation of telomere maintenance / protein sumoylation / protein serine/threonine kinase inhibitor activity / 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 / cytoplasm
Similarity search - Function
Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / : ...Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / : / E3 SUMO-protein ligase MMS21, N-terminal domain / DNA repair protein Nse5/Nse6 / DNA repair proteins Nse5 and Nse6 / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Non-structural maintenance of chromosomes element 4 / E3 SUMO-protein ligase MMS21 / DNA repair protein KRE29 / Non-structural maintenance of chromosome element 5 / Non-structural maintenance of chromosome element 3 / Non-structural maintenance of chromosomes element 1 / Structural maintenance of chromosomes protein 5 / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsQian, L. / Jun, Z. / Xiang, Z. / Tong, C. / Zhaoning, W. / Duo, J. / Zhenguo, C. / Lanfeng, W.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: 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
DepositionAug 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 5
B: Structural maintenance of chromosomes protein 6
C: E3 SUMO-protein ligase MMS21
D: DNA repair protein KRE29
E: Non-structural maintenance of chromosome element 5
F: Non-structural maintenance of chromosomes element 1
G: Non-structural maintenance of chromosome element 3
H: Non-structural maintenance of chromosomes element 4


Theoretical massNumber of molelcules
Total (without water)521,3168
Polymers521,3168
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB

#1: Protein Structural maintenance of chromosomes protein 5


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
#2: Protein Structural maintenance of chromosomes protein 6 / DNA repair protein RHC18 / Rad18 homolog


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

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Protein , 2 types, 2 molecules CD

#3: Protein E3 SUMO-protein ligase MMS21 / E3 SUMO-protein transferase MMS21 / Methyl methanesulfonate-sensitivity protein 21 / Non-structural ...E3 SUMO-protein transferase MMS21 / Methyl methanesulfonate-sensitivity protein 21 / Non-structural maintenance of chromosome element 2 / Non-SMC element 2


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
#4: Protein DNA repair protein KRE29 / Killer toxin-resistance protein 29


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

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Non-structural maintenance of chromosome element ... , 2 types, 2 molecules EG

#5: Protein Non-structural maintenance of chromosome element 5 / Non-SMC element 5


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
#7: Protein Non-structural maintenance of chromosome element 3 / Non-SMC element 3


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

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Non-structural maintenance of chromosomes element ... , 2 types, 2 molecules FH

#6: Protein Non-structural maintenance of chromosomes element 1 / Non-SMC element 1


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
#8: Protein Non-structural maintenance of chromosomes element 4


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

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of 8-subunit Smc5/6 / Type: COMPLEX / Entity ID: #1-#5, #8, #6-#7 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1056147 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00133978
ELECTRON MICROSCOPYf_angle_d0.3845741
ELECTRON MICROSCOPYf_dihedral_angle_d9.67313132
ELECTRON MICROSCOPYf_chiral_restr0.0365162
ELECTRON MICROSCOPYf_plane_restr0.0035906

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