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- EMDB-18378: Focused map for CSA-DDB1-DDA1 (map 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-18378
TitleFocused map for CSA-DDB1-DDA1 (map 2)
Map dataFocused map of CSA-DDB1-DDA1, sharpen
Sample
  • Complex: Ternary complex of CSA-DDB1-DDA1
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1- and DDB1-associated protein 1
KeywordsUbiquitin 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 / cullin family protein binding / viral release from host cell / response to X-ray / 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 / positive regulation of DNA repair / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / 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 / positive regulation of protein catabolic process / protein polyubiquitination / cellular response to UV / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / rhythmic process / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / DNA damage response / protein-containing complex binding / apoptotic process / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Det1 complexing ubiquitin ligase / : / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / G-protein beta WD-40 repeat ...DET1- and DDB1-associated protein 1, N-terminal / DET1- and DDB1-associated protein 1 / DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1 / Det1 complexing ubiquitin ligase / : / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / Mono-functional DNA-alkylating methyl methanesulfonate N-term / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / CPSF A subunit region / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA excision repair protein ERCC-8 / DNA damage-binding protein 1 / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLee S-H / Sixma TK
Funding support Netherlands, European Union, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)TOP 714.017.003 Netherlands
European Molecular Biology Organization (EMBO)ALTF 1159-2019European Union
CitationJournal: To Be Published
Title: Focused map for CSA-DDB1-DDA1 (map 2)
Authors: Lee S-H / Sixma TK
History
DepositionSep 1, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18378.png

Downloads & links

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Map

FileDownload / File: emd_18378.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of CSA-DDB1-DDA1, sharpen
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0017519805 - 2.0560787
Average (Standard dev.)0.0006631564 (±0.0193651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18378_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of CSA-DDB1-DDA1

EntireName: Ternary complex of CSA-DDB1-DDA1
Components
  • Complex: Ternary complex of CSA-DDB1-DDA1
    • Protein or peptide: DNA excision repair protein ERCC-8
    • Protein or peptide: DNA damage-binding protein 1
    • Protein or peptide: DET1- and DDB1-associated protein 1

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Supramolecule #1: Ternary complex of CSA-DDB1-DDA1

SupramoleculeName: Ternary complex of CSA-DDB1-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.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 190 KDa

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Macromolecule #1: DNA excision repair protein ERCC-8

MacromoleculeName: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHSA ALEVLFQGPG MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRPK GESKDLLFIL TAKYNACILE YKQSGESIDI ITRAHGNVQD RIGRPSETGI IGIIDPECRM IGLRLYDGLF KVIPLDRDNK ...String:
MAHHHHHHSA ALEVLFQGPG 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

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Macromolecule #3: DET1- and DDB1-associated protein 1

MacromoleculeName: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRKV ARTDSPDMHE DTDVLFQGPG AWSHPQFEKG GGSGGGSGGG SWSHPQFEKG ASGEDYKDDD DK

UniProtKB: DET1- and DDB1-associated protein 1

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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

Concentration0.13 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClsodium chloride
0.5 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: The grid was coated with graphene oxide
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was glutaraldehyde crosslinked

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
DetailsCollected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 723908
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.3.3) / Number images used: 122228
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: cryoSPARC, RELION (ver. 3.1.3))
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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