+Open data
-Basic information
Entry | Database: PDB / ID: 7t5p | |||||||||
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Title | Cryo-EM structure of human SIMC1-SLF2 complex | |||||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / Nse5 / Nse6 / SMC5 / SMC6 / SIMC1 / SLF2 / C5orf25 / viral restriction | |||||||||
Function / homology | Function and homology information positive regulation of maintenance of mitotic sister chromatid cohesion / SUMO polymer binding / negative regulation of peptidase activity / Smc5-Smc6 complex / peptidase inhibitor activity / protein localization to site of double-strand break / positive regulation of double-strand break repair / regulation of telomere maintenance / protein sumoylation / sarcomere ...positive regulation of maintenance of mitotic sister chromatid cohesion / SUMO polymer binding / negative regulation of peptidase activity / Smc5-Smc6 complex / peptidase inhibitor activity / protein localization to site of double-strand break / positive regulation of double-strand break repair / regulation of telomere maintenance / protein sumoylation / sarcomere / double-strand break repair via homologous recombination / positive regulation of protein-containing complex assembly / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Maeda, S. / Oravcova, M. / Boddy, M.N. / Otomo, T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t5p.cif.gz | 295.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t5p.ent.gz | 235.4 KB | Display | PDB format |
PDBx/mmJSON format | 7t5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t5p_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7t5p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7t5p_validation.xml.gz | 35.6 KB | Display | |
Data in CIF | 7t5p_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/7t5p ftp://data.pdbj.org/pub/pdb/validation_reports/t5/7t5p | HTTPS FTP |
-Related structure data
Related structure data | 25706MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human SIMC1-SLF2 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 88 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39826 / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |