+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18380 | |||||||||
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Title | Focused map for UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1 | |||||||||
Map data | Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS), sharpen | |||||||||
Sample |
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Keywords | Ubiquitin ligase DNA repair / LIGASE | |||||||||
Function / homology | Function and homology information regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont ...regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / single strand break repair / positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II complex binding / cullin family protein binding / viral release from host cell / response to X-ray / positive regulation of DNA repair / ectopic germ cell programmed cell death / proteasomal protein catabolic process / protein autoubiquitination / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / regulation of circadian rhythm / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Wnt signaling pathway / Formation of Incision Complex in GG-NER / nuclear matrix / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / rhythmic process / chromosome / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / chromosome, telomeric region / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / damaged DNA binding / protein ubiquitination / DNA repair / DNA damage response / negative regulation of apoptotic process / protein-containing complex binding / nucleolus / apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Lee S-H / Sixma TK | |||||||||
Funding support | Netherlands, European Union, 2 items
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Citation | Journal: To Be Published Title: Focused map for UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1 Authors: Lee S-H / Sixma TK | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18380.map.gz | 111.8 MB | EMDB map data format | |
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Header (meta data) | emd-18380-v30.xml emd-18380.xml | 24.4 KB 24.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18380_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_18380.png | 55 KB | ||
Masks | emd_18380_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-18380.cif.gz | 6.9 KB | ||
Others | emd_18380_additional_1.map.gz emd_18380_half_map_1.map.gz emd_18380_half_map_2.map.gz | 97.8 MB 98.7 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18380 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18380 | HTTPS FTP |
-Validation report
Summary document | emd_18380_validation.pdf.gz | 691 KB | Display | EMDB validaton report |
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Full document | emd_18380_full_validation.pdf.gz | 690.5 KB | Display | |
Data in XML | emd_18380_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_18380_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18380 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18380 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18380.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS), sharpen | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18380_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS),raw map
File | emd_18380_additional_1.map | ||||||||||||
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Annotation | Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS),raw map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS),half map 1
File | emd_18380_half_map_1.map | ||||||||||||
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Annotation | Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS),half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS),half map 2
File | emd_18380_half_map_2.map | ||||||||||||
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Annotation | Focused map of CSA-DDB1(BPA/BPC)-DDA1-UVSSA(VHS),half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1
Entire | Name: Ternary complex of UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1 |
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Components |
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-Supramolecule #1: Ternary complex of UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1
Supramolecule | Name: Ternary complex of UVSSA(VHS)-CSA-DDB1(BPA/BPC)-DDA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Ternary complex of ubiquitinated UVSSA-USP7-CSA-DDB1-DDA1. Refinement focused on CSA-DDB1-DDA1. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 170 KDa |
-Macromolecule #1: DNA excision repair protein ERCC-8
Macromolecule | Name: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCSI GRDHPDVHRY SVETVQWYPH DTGMFTSSSF DKTLKVWDTN TLQTADVFNF EETVYSHHMS PVSTKHCLVA VGTRGPKVQL ...String: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCSI GRDHPDVHRY SVETVQWYPH DTGMFTSSSF DKTLKVWDTN TLQTADVFNF EETVYSHHMS PVSTKHCLVA VGTRGPKVQL CDLKSGSCSH ILQGHRQEIL AVSWSPRYDY ILATASADSR VKLWDVRRAS GCLITLDQHN GKKSQAVESA NTAHNGKVNG LCFTSDGLHL LTVGTDNRMR LWNSSNGENT LVNYGKVCNN SKKGLKFTVS CGCSSEFVFV PYGSTIAVYT VYSGEQITML KGHYKTVDCC VFQSNFQELY SGSRDCNILA WVPSLYEPVP DDDETTTKSQ LNPAFEDAWS SSDEEGGTSA WSHPQFEK UniProtKB: DNA excision repair protein ERCC-8 |
-Macromolecule #2: DNA damage-binding protein 1
Macromolecule | Name: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL ...String: MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ELKAFNIRLE ELHVIDVKFL YGCQAPTICF VYQDPQGRHV KTYEVSLREK EFNKGPWKQE NVEAEASMVI AVPEPFGGAI IIGQESITYH NGDKYLAIAP PIIKQSTIVC HNRVDPNGSR YLLGDMEGRL FMLLLEKEEQ MDGTVTLKDL RVELLGETSI AECLTYLDNG VVFVGSRLGD SQLVKLNVDS NEQGSYVVAM ETFTNLGPIV DMCVVDLERQ GQGQLVTCSG AFKEGSLRII RNGIGIHEHA SIDLPGIKGL WPLRSDPNRE TDDTLVLSFV GQTRVLMLNG EEVEETELMG FVDDQQTFFC GNVAHQQLIQ ITSASVRLVS QEPKALVSEW KEPQAKNISV ASCNSSQVVV AVGRALYYLQ IHPQELRQIS HTEMEHEVAC LDITPLGDSN GLSPLCAIGL WTDISARILK LPSFELLHKE MLGGEIIPRS ILMTTFESSH YLLCALGDGA LFYFGLNIET GLLSDRKKVT LGTQPTVLRT FRSLSTTNVF ACSDRPTVIY SSNHKLVFSN VNLKEVNYMC PLNSDGYPDS LALANNSTLT IGTIDEIQKL HIRTVPLYES PRKICYQEVS QCFGVLSSRI EVQDTSGGTT ALRPSASTQA LSSSVSSSKL FSSSTAPHET SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGAV YSMVEFNGKL LASINSTVRL YEWTTEKELR TECNHYNNIM ALYLKTKGDF ILVGDLMRSV LLLAYKPMEG NFEEIARDFN PNWMSAVEIL DDDNFLGAEN AFNLFVCQKD SAATTDEERQ HLQEVGLFHL GEFVNVFCHG SLVMQNLGET STPTQGSVLF GTVNGMIGLV TSLSESWYNL LLDMQNRLNK VIKSVGKIEH SFWRSFHTER KTEPATGFID GDLIESFLDI SRPKMQEVVA NLQYDDGSGM KREATADDLI KVVEELTRIH UniProtKB: DNA damage-binding protein 1 |
-Macromolecule #3: DET1- and DDB1-associated protein 1
Macromolecule | Name: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRKV ARTDSPDMHE DTDVLFQGPG AWSHPQFEKG GGSGGGSGGG SWSHPQFEKG ASGEDYKDDD DK UniProtKB: DET1- and DDB1-associated protein 1 |
-Macromolecule #4: UV-stimulated scaffold protein A
Macromolecule | Name: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 4 / Details: K414 is ubiquitinated / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAHHHHHHSA ALEVLFQGPG MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLELT LGTDPAQPLP PPREAAQRLR QATTRAVEGW NEKFGEAYKK LALGYHFLRH NKKVDFQDTN ...String: MAHHHHHHSA ALEVLFQGPG MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELFV RSHQFRMLVV SNFQEFLELT LGTDPAQPLP PPREAAQRLR QATTRAVEGW NEKFGEAYKK LALGYHFLRH NKKVDFQDTN ARSLAERKRE EEKQKHLDKI YQERASQAER EMQEMSGEIE SCLTEVESCF RLLVPFDFDP NPETESLGMA SGMSDALRSS CAGQVGPCRS GTPDPRDGEQ PCCSRDLPAS AGHPRAGGGA QPSQTATGDP SDEDEDSDLE EFVRSHGLGS HKYTLDVELC SEGLKVQENE DNLALIHAAR DTLKLIRNKF LPAVCSWIQR FTRVGTHGGC LKRAIDLKAE LELVLRKYKE LDIEPEGGER RRTEALGDAE EDEDDEDFVE VPEKEGYEPH IPDHLRPEYG LEAAPEKDTV VRCLRTRTRM DEEVSDPTSA AAQLRQLRDH LPPPSSASPS RALPEPQEAQ KLAAERARAP VVPYGVDLHY WGQELPTAGK IVKSDSQHRF WKPSEVEEEV VNADISEMLR SRHITFAGKF EPVQHWCRAP RPDGRLCERQ DRLKCPFHGK IVPRDDEGRP LDPEDRAREQ RRQLQKQERP EWQDPELMRD VEAATGQDLG SSRYSGKGRG KKRRYPSLTN LKAQADTARA RIGRKVFAKA AVRRVVAAMN RMDQKKHEKF SNQFNYALN UniProtKB: UV-stimulated scaffold protein A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.13 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Details: The grid was coated with graphene oxide | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | This sample was glutaraldehyde crosslinked |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Details | Collected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN) |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1382 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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