+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25706 | |||||||||
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Title | Cryo-EM structure of human SIMC1-SLF2 complex | |||||||||
Map data | sharpened | |||||||||
Sample |
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Keywords | Nse5 / Nse6 / SMC5 / SMC6 / SIMC1 / SLF2 / C5orf25 / viral restriction / ANTIVIRAL PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Maeda S / Oravcova M | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25706.map.gz | 27.1 MB | EMDB map data format | |
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Header (meta data) | emd-25706-v30.xml emd-25706.xml | 19.3 KB 19.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25706_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_25706.png | 83.6 KB | ||
Filedesc metadata | emd-25706.cif.gz | 6.1 KB | ||
Others | emd_25706_additional_1.map.gz emd_25706_half_map_1.map.gz emd_25706_half_map_2.map.gz | 23.5 MB 23.4 MB 23.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25706 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25706 | HTTPS FTP |
-Validation report
Summary document | emd_25706_validation.pdf.gz | 731.5 KB | Display | EMDB validaton report |
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Full document | emd_25706_full_validation.pdf.gz | 731 KB | Display | |
Data in XML | emd_25706_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_25706_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25706 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25706 | HTTPS FTP |
-Related structure data
Related structure data | 7t5pMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25706.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.134 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: non-sharpened
File | emd_25706_additional_1.map | ||||||||||||
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Annotation | non-sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_25706_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_25706_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human SIMC1-SLF2 complex
Entire | Name: Human SIMC1-SLF2 complex |
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Components |
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-Supramolecule #1: Human SIMC1-SLF2 complex
Supramolecule | Name: Human SIMC1-SLF2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: SUMO-interacting motif-containing protein 1
Macromolecule | Name: SUMO-interacting motif-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 67.021539 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: SMC5-SMC6 complex localization factor protein 2
Macromolecule | Name: SMC5-SMC6 complex localization factor protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.867793 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7t5p: |