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- EMDB-25706: Cryo-EM structure of human SIMC1-SLF2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-25706
TitleCryo-EM structure of human SIMC1-SLF2 complex
Map datasharpened
Sample
  • Complex: Human SIMC1-SLF2 complex
    • Protein or peptide: SUMO-interacting motif-containing protein 1
    • Protein or peptide: SMC5-SMC6 complex localization factor protein 2
KeywordsNse5 / Nse6 / SMC5 / SMC6 / SIMC1 / SLF2 / C5orf25 / viral restriction / ANTIVIRAL PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMaeda S / Oravcova M
Funding support United States, 2 items
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, 2021-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25706.png

Downloads & links

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Map

FileDownload / File: emd_25706.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 200 pix.
= 226.8 Å		1.13 Å/pix.
x 200 pix.
= 226.8 Å		1.13 Å/pix.
x 200 pix.
= 226.8 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.134 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.0006515504 - 2.1476994
Average (Standard dev.)0.0036779365 (±0.048465557)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 226.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: non-sharpened

Fileemd_25706_additional_1.map
Annotationnon-sharpened
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: half map 1

Fileemd_25706_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_25706_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Sample components

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Entire : Human SIMC1-SLF2 complex

EntireName: Human SIMC1-SLF2 complex
Components
  • Complex: Human SIMC1-SLF2 complex
    • Protein or peptide: SUMO-interacting motif-containing protein 1
    • Protein or peptide: SMC5-SMC6 complex localization factor protein 2

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Supramolecule #1: Human SIMC1-SLF2 complex

SupramoleculeName: Human SIMC1-SLF2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SUMO-interacting motif-containing protein 1

MacromoleculeName: SUMO-interacting motif-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.021539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AYLQDMPRSP GDVPQSPSDV SPSPDAPQSP GGMPHLPGDV LHSPGDMPHS SGDVTHSPRD IPHLPGDRPD FTQNDVQNRD MPMDISALS SPSCSPRPQS ETPLEKVPWL SVMETPARKE ISLSEPAKPG SAHVQSRTPQ GGLYNRPCLH RLKYFLRPPV H HLFFQTLI ...String:
AYLQDMPRSP GDVPQSPSDV SPSPDAPQSP GGMPHLPGDV LHSPGDMPHS SGDVTHSPRD IPHLPGDRPD FTQNDVQNRD MPMDISALS SPSCSPRPQS ETPLEKVPWL SVMETPARKE ISLSEPAKPG SAHVQSRTPQ GGLYNRPCLH RLKYFLRPPV H HLFFQTLI PDKDTRENKG QRLEPIPHRR LRMVTNTIEE NFPLGTVQFL MDFVSPQHYP PREIVAHIIQ KILLSGSETV DV LKEAYML LMKIQQLHPA NAKTVEWDWK LLTYVMEEEG QTLPGRVLFL RYVVQTLEDD FQQTLRRQRQ HLQQSIANMV LSC DKQPHN VRDVIKWLVK AVTEDGLTQP PNGNQTSSGT GILKASSSHP SSQPNLTKNT NQLIVCQLQR MLSIAVEVDR TPTC SSNKI AEMMFGFVLD IPERSQREMF FTTMESHLLR CKVLEIIFLH SCETPTRLPL SLAQALYFLN NSTSLLKCQS DKSQW QTWD ELVERLQFLL SSYQHVLREH LRSSVIDRKD LIIKRIKPKP QQGDDITVVD VEKQIEAFRS RLIQMLGEPL VPQLQD KVH LLKLLLFYAA DLNPDAEPFQ KGWSGS

UniProtKB: SUMO-interacting motif-containing protein 1

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Macromolecule #2: SMC5-SMC6 complex localization factor protein 2

MacromoleculeName: SMC5-SMC6 complex localization factor protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.867793 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TPAATGKPPA LSKGLRSQSS DYTGHVHPGT YTNTLERLVK EMEDTQRLDE LQKQLQEDIR QGRGIKSPIR IGEEDSTDDE DGLLEEHKE FLKKFSVTID AIPDHHPGEE IFNFLNSGKI FNQYTLDLRD SGFIGQSAVE KLILKSGKTD QIFLTTQGFL T SAYHYVQC ...String:
TPAATGKPPA LSKGLRSQSS DYTGHVHPGT YTNTLERLVK EMEDTQRLDE LQKQLQEDIR QGRGIKSPIR IGEEDSTDDE DGLLEEHKE FLKKFSVTID AIPDHHPGEE IFNFLNSGKI FNQYTLDLRD SGFIGQSAVE KLILKSGKTD QIFLTTQGFL T SAYHYVQC PVPVLKWLFR MMSVHTDCIV SVQILSTLME ITIRNDTFSD SPVWPWIPSL SDVAAVFFNM GIDFRSLFPL EN LQPDFNE DYLVSETQTT SRGKESEDSS YKPIFSTLPE TNILNVVKFL GLCTSIHPEG YQDREIMLLI LMLFKMSLEK QLK QIPLVD FQSLLINLMK NIRDWNTKVP ELCLGINELS SHPHNLLWLV QLVPNWTSRG RQLRQCLSLV IISKLLDEKH EDVP NASNL QVSVLHRYLV QMKPSDLLKK MVLKKKAEQP DGIIDDSLHL ELEKQAYYLT YILLHLVGEV SCSHSFSSGQ RKHFV LLCG ALEKHVKCDI REDARLFYRT KVKDLVARIH GKWQEIIQNC RPTQGQLHDF WVPDS

UniProtKB: SMC5-SMC6 complex localization factor protein 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 73000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 39826
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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