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- PDB-7ymd: Cryo-EM structure of Nse1/3/4 -

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Basic information

Entry
Database: PDB / ID: 7ymd
TitleCryo-EM structure of Nse1/3/4
Components
  • Non-structural maintenance of chromosome element 3
  • Non-structural maintenance of chromosome element 4
  • Non-structural maintenance of chromosomes element 1
KeywordsCELL CYCLE
Function / homology
Function and homology information


Smc5-Smc6 complex / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / chromatin looping / DNA damage tolerance / regulation of telomere maintenance / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / chromosome, telomeric region ...Smc5-Smc6 complex / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / chromatin looping / DNA damage tolerance / regulation of telomere maintenance / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / chromosome, telomeric region / DNA repair / zinc ion 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 / MAGE homology domain ...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 / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Non-structural maintenance of chromosome element 4 / Non-structural maintenance of chromosome element 3 / Non-structural maintenance of chromosomes element 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.176 Å
AuthorsQian, L. / Jun, Z. / 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
DepositionJul 28, 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: Non-structural maintenance of chromosome element 4
B: Non-structural maintenance of chromosomes element 1
C: Non-structural maintenance of chromosome element 3


Theoretical massNumber of molelcules
Total (without water)118,5753
Polymers118,5753
Non-polymers00
Water00
1


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

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Components

#1: Protein Non-structural maintenance of chromosome element 4 / Non-SMC element 4 / Protein QRI2


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: Escherichia coli (E. coli) / References: UniProt: P43124
#2: 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: Escherichia coli (E. coli)
References: UniProt: Q07913, RING-type E3 ubiquitin transferase
#3: 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: Escherichia coli (E. coli) / References: UniProt: Q05541
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 Nse1/3/4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c
Source (recombinant)Organism: Escherichia coli (E. coli)
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: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.176 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 610732 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0015746
ELECTRON MICROSCOPYf_angle_d0.3587753
ELECTRON MICROSCOPYf_dihedral_angle_d9.4962146
ELECTRON MICROSCOPYf_chiral_restr0.037885
ELECTRON MICROSCOPYf_plane_restr0.003993

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