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- PDB-7t5p: Cryo-EM structure of human SIMC1-SLF2 complex -

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Basic information

Entry
Database: PDB / ID: 7t5p
TitleCryo-EM structure of human SIMC1-SLF2 complex
Components
  • SMC5-SMC6 complex localization factor protein 2
  • SUMO-interacting motif-containing protein 1
KeywordsANTIVIRAL PROTEIN / Nse5 / Nse6 / SMC5 / SMC6 / SIMC1 / SLF2 / C5orf25 / viral restriction
Function / homology
Function and homology information


SUMO polymer binding / positive regulation of maintenance of mitotic sister chromatid cohesion / Smc5-Smc6 complex / peptidase inhibitor activity / chromatin looping / protein localization to site of double-strand break / regulation of telomere maintenance / positive regulation of double-strand break repair / protein sumoylation / sarcomere ...SUMO polymer binding / positive regulation of maintenance of mitotic sister chromatid cohesion / Smc5-Smc6 complex / peptidase inhibitor activity / chromatin looping / protein localization to site of double-strand break / regulation of telomere maintenance / positive regulation of double-strand break repair / protein sumoylation / sarcomere / positive regulation of protein-containing complex assembly / double-strand break repair via homologous recombination / PML body / site of double-strand break / chromosome, telomeric region / intracellular membrane-bounded organelle / DNA damage response / ubiquitin protein ligase binding / chromatin / protein-containing complex binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
FAM178 family / Coiled-coil SMC6 And NSE5 INteracting (CANIN) domain / Coiled-coil and Nse Interacting (CANIN) domain / :
Similarity search - Domain/homology
SMC5-SMC6 complex localization factor protein 2 / SUMO-interacting motif-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMaeda, S. / Oravcova, M. / Boddy, M.N. / Otomo, T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM092740 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136273 United States
CitationJournal: Elife / Year: 2022
Title: The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers.
Authors: Martina Oravcová / Minghua Nie / Nicola Zilio / Shintaro Maeda / Yasaman Jami-Alahmadi / Eros Lazzerini-Denchi / James A Wohlschlegel / Helle D Ulrich / Takanori Otomo / Michael N Boddy /
Abstract: The human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 ...The human SMC5/6 complex is a conserved guardian of genome stability and an emerging component of antiviral responses. These disparate functions likely require distinct mechanisms of SMC5/6 regulation. In yeast, Smc5/6 is regulated by its Nse5/6 subunits, but such regulatory subunits for human SMC5/6 are poorly defined. Here, we identify a novel SMC5/6 subunit called SIMC1 that contains SUMO interacting motifs (SIMs) and an Nse5-like domain. We isolated SIMC1 from the proteomic environment of SMC5/6 within polyomavirus large T antigen (LT)-induced subnuclear compartments. SIMC1 uses its SIMs and Nse5-like domain to localize SMC5/6 to polyomavirus replication centers (PyVRCs) at SUMO-rich PML nuclear bodies. SIMC1's Nse5-like domain binds to the putative Nse6 orthologue SLF2 to form an anti-parallel helical dimer resembling the yeast Nse5/6 structure. SIMC1-SLF2 structure-based mutagenesis defines a conserved surface region containing the N-terminus of SIMC1's helical domain that regulates SMC5/6 localization to PyVRCs. Furthermore, SLF1, which recruits SMC5/6 to DNA lesions via its BRCT and ARD motifs, binds SLF2 analogously to SIMC1 and forms a separate Nse5/6-like complex. Thus, two Nse5/6-like complexes with distinct recruitment domains control human SMC5/6 localization.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUMO-interacting motif-containing protein 1
B: SMC5-SMC6 complex localization factor protein 2


Theoretical massNumber of molelcules
Total (without water)128,8892
Polymers128,8892
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4990 Å2
ΔGint-30 kcal/mol
Surface area39200 Å2

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Components

#1: Protein SUMO-interacting motif-containing protein 1 / Platform element for inhibition of autolytic degradation


Mass: 67021.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIMC1, C5orf25, PLEIAD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NDZ2
#2: Protein SMC5-SMC6 complex localization factor protein 2 / Smc5/6 localization factor 1


Mass: 61867.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLF2, C10orf6, FAM178A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IX21

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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: Human SIMC1-SLF2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 88 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 73000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2Leginonimage acquisition
4GctfCTF correction
7Cootmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39826 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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