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- EMDB-18398: CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 -

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Basic information

Entry
Database: EMDB / ID: EMD-18398
TitleCryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1
Map dataComposite map of UVSSA(VHS)-CSA-DDB1-DDA1
Sample
  • Complex: Ternary complex of UVSSA(VHS)-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
    • Protein or peptide: UV-stimulated scaffold protein A
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 / double-strand break repair via classical nonhomologous end joining / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / 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 / double-strand break repair via classical nonhomologous end joining / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / 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 / ectopic germ cell programmed cell death / positive regulation of viral genome replication / proteasomal protein catabolic process / transcription-coupled nucleotide-excision repair / response to UV / protein autoubiquitination / positive regulation of gluconeogenesis / positive regulation of DNA repair / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / regulation of circadian rhythm / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / nuclear matrix / Dual incision in TC-NER / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / rhythmic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / Neddylation / chromosome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / response to oxidative stress / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / 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 / ENTH/VHS ...UV-stimulated scaffold protein A / : / : / Uncharacterized conserved protein (DUF2043) / UVSSA N-terminal domain / 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 / ENTH/VHS / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 / UV-stimulated scaffold protein A / DET1- and DDB1-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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: CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1
Authors: Lee S-H / Sixma TK
History
DepositionSep 6, 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_18398.png

Downloads & links

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Map

FileDownload / File: emd_18398.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of UVSSA(VHS)-CSA-DDB1-DDA1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 320 pix.
= 338.24 Å		1.06 Å/pix.
x 320 pix.
= 338.24 Å		1.06 Å/pix.
x 320 pix.
= 338.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.057 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.828
Minimum - Maximum-1.8985326 - 85.661789999999996
Average (Standard dev.)0.0013382172 (±0.94812536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 338.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1

EntireName: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1
Components
  • Complex: Ternary complex of UVSSA(VHS)-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
    • Protein or peptide: UV-stimulated scaffold protein A

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Supramolecule #1: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1

SupramoleculeName: Ternary complex of UVSSA(VHS)-CSA-DDB1-DDA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4, #1
Details: Ternary complex of ubiquitinated UVSSA-USP7-CSA-DDB1-DDA1. USP7 is invisible in the cryoEM map.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: UV-stimulated scaffold protein A

MacromoleculeName: UV-stimulated scaffold protein A / type: protein_or_peptide / ID: 1 / Details: The construct contains an N-terminal His tag. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.923164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHSA ALEVLFQGPG MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELF VRSHQFRMLV VSNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR H NKKVDFQD ...String:
MAHHHHHHSA ALEVLFQGPG MDQKLSKLVE ELTTSGEPRL NPEKMKELKK ICKSSEEQLS RAYRLLIAQL TQEHAEIRLS AFQIVEELF VRSHQFRMLV VSNFQEFLEL TLGTDPAQPL PPPREAAQRL RQATTRAVEG WNEKFGEAYK KLALGYHFLR H NKKVDFQD TNARSLAERK REEEKQKHLD KIYQERASQA EREMQEMSGE IESCLTEVES CFRLLVPFDF DPNPETESLG MA SGMSDAL RSSCAGQVGP CRSGTPDPRD GEQPCCSRDL PASAGHPRAG GGAQPSQTAT GDPSDEDEDS DLEEFVRSHG LGS HKYTLD VELCSEGLKV QENEDNLALI HAARDTLKLI RNKFLPAVCS WIQRFTRVGT HGGCLKRAID LKAELELVLR KYKE LDIEP EGGERRRTEA LGDAEEDEDD EDFVEVPEKE GYEPHIPDHL RPEYGLEAAP EKDTVVRCLR TRTRMDEEVS DPTSA AAQL RQLRDHLPPP SSASPSRALP EPQEAQKLAA ERARAPVVPY GVDLHYWGQE LPTAGKIVKS DSQHRFWKPS EVEEEV VNA DISEMLRSRH ITFAGKFEPV QHWCRAPRPD GRLCERQDRL KCPFHGKIVP RDDEGRPLDP EDRAREQRRQ LQKQERP EW QDPELMRDVE AATGQDLGSS RYSGKGRGKK RRYPSLTNLK AQADTARARI GRKVFAKAAV RRVVAAMNRM DQKKHEKF S NQFNYALN

UniProtKB: UV-stimulated scaffold protein A

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Macromolecule #2: DNA excision repair protein ERCC-8

MacromoleculeName: DNA excision repair protein ERCC-8 / type: protein_or_peptide / ID: 2
Details: The construct contains a Strep tag II at the C-terminus
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.465613 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV ...String:
MLGFLSARQT GLEDPLRLRR AESTRRVLGL ELNKDRDVER IHGGGINTLD IEPVEGRYML SGGSDGVIVL YDLENSSRQS YYTCKAVCS IGRDHPDVHR YSVETVQWYP HDTGMFTSSS FDKTLKVWDT NTLQTADVFN FEETVYSHHM SPVSTKHCLV A VGTRGPKV QLCDLKSGSC SHILQGHRQE ILAVSWSPRY DYILATASAD SRVKLWDVRR ASGCLITLDQ HNGKKSQAVE SA NTAHNGK VNGLCFTSDG LHLLTVGTDN RMRLWNSSNG ENTLVNYGKV CNNSKKGLKF TVSCGCSSEF VFVPYGSTIA VYT VYSGEQ ITMLKGHYKT VDCCVFQSNF QELYSGSRDC NILAWVPSLY EPVPDDDETT TKSQLNPAFE DAWSSSDEEG GTSA WSHPQ FEK

UniProtKB: DNA excision repair protein ERCC-8

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Macromolecule #3: DNA damage-binding protein 1

MacromoleculeName: DNA damage-binding protein 1 / type: protein_or_peptide / ID: 3 / Details: The construct contains an N-terminal His tag. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 129.298867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHSA ALEVLFQGPG MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRP KGESKDLLFI LTAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL F KVIPLDRD ...String:
MAHHHHHHSA ALEVLFQGPG MSYNYVVTAQ KPTAVNGCVT GHFTSAEDLN LLIAKNTRLE IYVVTAEGLR PVKEVGMYGK IAVMELFRP KGESKDLLFI LTAKYNACIL EYKQSGESID IITRAHGNVQ DRIGRPSETG IIGIIDPECR MIGLRLYDGL F KVIPLDRD NKELKAFNIR LEELHVIDVK FLYGCQAPTI CFVYQDPQGR HVKTYEVSLR EKEFNKGPWK QENVEAEASM VI AVPEPFG GAIIIGQESI TYHNGDKYLA IAPPIIKQST IVCHNRVDPN GSRYLLGDME GRLFMLLLEK EEQMDGTVTL KDL RVELLG ETSIAECLTY LDNGVVFVGS RLGDSQLVKL NVDSNEQGSY VVAMETFTNL GPIVDMCVVD LERQGQGQLV TCSG AFKEG SLRIIRNGIG IHEHASIDLP GIKGLWPLRS DPNRETDDTL VLSFVGQTRV LMLNGEEVEE TELMGFVDDQ QTFFC GNVA HQQLIQITSA SVRLVSQEPK ALVSEWKEPQ AKNISVASCN SSQVVVAVGR ALYYLQIHPQ ELRQISHTEM EHEVAC LDI TPLGDSNGLS PLCAIGLWTD ISARILKLPS FELLHKEMLG GEIIPRSILM TTFESSHYLL CALGDGALFY FGLNIET GL LSDRKKVTLG TQPTVLRTFR SLSTTNVFAC SDRPTVIYSS NHKLVFSNVN LKEVNYMCPL NSDGYPDSLA LANNSTLT I GTIDEIQKLH IRTVPLYESP RKICYQEVSQ CFGVLSSRIE VQDTSGGTTA LRPSASTQAL SSSVSSSKLF SSSTAPHET SFGEEVEVHN LLIIDQHTFE VLHAHQFLQN EYALSLVSCK LGKDPNTYFI VGTAMVYPEE AEPKQGRIVV FQYSDGKLQT VAEKEVKGA VYSMVEFNGK LLASINSTVR LYEWTTEKEL RTECNHYNNI MALYLKTKGD FILVGDLMRS VLLLAYKPME G NFEEIARD FNPNWMSAVE ILDDDNFLGA ENAFNLFVCQ KDSAATTDEE RQHLQEVGLF HLGEFVNVFC HGSLVMQNLG ET STPTQGS VLFGTVNGMI GLVTSLSESW YNLLLDMQNR LNKVIKSVGK IEHSFWRSFH TERKTEPATG FIDGDLIESF LDI SRPKMQ EVVANLQYDD GSGMKREATA DDLIKVVEEL TRIH

UniProtKB: DNA damage-binding protein 1

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Macromolecule #4: DET1- and DDB1-associated protein 1

MacromoleculeName: DET1- and DDB1-associated protein 1 / type: protein_or_peptide / ID: 4
Details: The construct contains a TwinStrep tag and a Flag tag at the C-terminus.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.997615 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MADFLKGLPV YNKSNFSRFH ADSVCKASNR RPSVYLPTRE YPSEQIIVTE KTNILLRYLH QQWDKKNAAK KRDQEQVELE GESSAPPRK VARTDSPDMH EDTDVLFQGP GAWSHPQFEK GGGSGGGSGG GSWSHPQFEK GASGEDYKDD DDK

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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.3.3)
Details: Combined from focused maps reconstructed with various particle numbers.
Number images used: 294142
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)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7oo3

chain_id: P, residue_range: 1-396, source_name: PDB, initial_model_type: experimental modelCSA

7oo3

chain_id: T, residue_range: 1-1140, source_name: PDB, initial_model_type: experimental modelDDB1(BPA/BPC)

6zx9

chain_id: A, residue_range: 393-709, source_name: PDB, initial_model_type: experimental modelDDB1(BPB)

6ud7

chain_id: D, residue_range: 4-76, source_name: PDB, initial_model_type: experimental modelDDA1

yd98

chain_id: A, residue_range: 1-150, source_name: AlphaFold, initial_model_type: in silico modelUVSSA(VHS)
DetailsAdditional densities are observed near several cysteine residues (A/Cys222, A/Cys260, A/Cys288, B/Cys363, B/Cys725, B/Cys1008). We expect these are oxidized products or crosslinking side products.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qh5:
CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1

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