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- PDB-8i4x: Cryo-EM structure of 5-subunit Smc5/6 -

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Basic information

Entry
Database: PDB / ID: 8i4x
TitleCryo-EM structure of 5-subunit Smc5/6
Components
  • E3 SUMO-protein ligase MMS21
  • Non-structural maintenance of chromosome element 5
  • Nse6
  • Structural maintenance of chromosomes protein 5
  • Structural maintenance of chromosomes protein 6
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 / SUMOylation of DNA damage response and repair proteins / ATPase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / chromosome separation / SUMOylation of DNA damage response and repair proteins / ATPase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / recombinational repair / regulation of telomere maintenance / protein sumoylation / protein serine/threonine kinase inhibitor activity / double-strand break repair via homologous recombination / nuclear envelope / single-stranded DNA binding / site of double-strand break / damaged DNA binding / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / mitochondrion / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / 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. / Rad50/SbcC-type AAA domain / AAA domain ...: / 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. / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 SUMO-protein ligase MMS21 / DNA repair protein KRE29 / Non-structural maintenance of chromosome element 5 / 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: 8.5 Å
AuthorsQian, L. / Jun, Z. / Xiang, Z. / Zhaoning, W. / Tong, C. / Duo, J. / Zhenguo, C. / Wang, L.
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
DepositionJan 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _em_admin.last_update
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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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: Nse6
E: Non-structural maintenance of chromosome element 5


Theoretical massNumber of molelcules
Total (without water)389,2465
Polymers389,2465
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27180 Å2
ΔGint-105 kcal/mol
Surface area164700 Å2

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Components

#1: Protein Structural maintenance of chromosomes protein 5


Mass: 123390.031 Da / Num. of mol.: 1 / Mutation: M824A
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: 126889.375 Da / Num. of mol.: 1 / Mutation: L464A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: SMC6, RHC18, YLR383W, L3502.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12749
#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: MMS21, NSE2, YEL019C / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P38632, Transferases; Acyltransferases; Aminoacyltransferases
#4: Protein Nse6


Mass: 44498.242 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
#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) / Gene: NSE5, YML023C / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q03718
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 5-subunit Smc5/6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288C
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268567 / Symmetry type: POINT

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