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- PDB-7v7b: CryoEM structure of DDB1-VprBP complex in ARM-up conformation -

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Basic information

Entry
Database: PDB / ID: 7v7b
TitleCryoEM structure of DDB1-VprBP complex in ARM-up conformation
Components
  • DDB1- and CUL4-associated factor 1
  • DNA damage-binding protein 1
KeywordsTRANSFERASE/DNA BINDING PROTEIN / Ubiquitin pathway / E3 ligase / Substrate recognition unit / LIGASE / TRANSFERASE-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


cell competition in a multicellular organism / histone H2AT120 kinase activity / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition ...cell competition in a multicellular organism / histone H2AT120 kinase activity / V(D)J recombination / positive regulation by virus of viral protein levels in host cell / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cytokinesis / regulation of mitotic cell cycle phase transition / regulation of miRNA-mediated gene silencing / regulation of natural killer cell activation / WD40-repeat domain binding / nucleotide-excision repair complex / Cul4-RING E3 ubiquitin ligase complex / regulation of cell cycle phase transition / regulation of stem cell population maintenance / ubiquitin ligase complex scaffold activity / negative regulation of adipose tissue development / Cul4B-RING E3 ubiquitin ligase complex / regulation of cellular response to stress / viral release from host cell / Cul4A-RING E3 ubiquitin ligase complex / cullin family protein binding / regulation of DNA-templated DNA replication initiation / positive regulation of viral genome replication / B cell differentiation / ubiquitin-like ligase-substrate adaptor activity / positive regulation of gluconeogenesis / post-translational protein modification / regulation of embryonic development / replication fork processing / nuclear estrogen receptor binding / proteasomal protein catabolic process / epigenetic regulation of gene expression / nucleotide-excision repair / regulation of autophagy / Recognition of DNA damage by PCNA-containing replication complex / fibrillar center / regulation of circadian rhythm / cell population proliferation / 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 / Formation of Incision Complex in GG-NER / cellular response to UV / Dual incision in TC-NER / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / Antigen processing: Ubiquitination & Proteasome degradation / site of double-strand break / regulation of cell population proliferation / Neddylation / spermatogenesis / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / regulation of apoptotic process / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein-macromolecule adaptor activity / protein ubiquitination / DNA repair / protein serine kinase activity / centrosome / DNA damage response / nucleolus / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / nucleoplasm / extracellular region / nucleus / cytoplasm
Similarity search - Function
VPRBP/DCAF1 family / : / : / : / : / DCAF1 helical domain / DCAF1 fourth domain / Mahjong helical domain / DCAF1 N-terminal domain / Lissencephaly type-1-like homology motif ...VPRBP/DCAF1 family / : / : / : / : / DCAF1 helical domain / DCAF1 fourth domain / Mahjong helical domain / DCAF1 N-terminal domain / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / : / 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 / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA damage-binding protein 1 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang, D. / Xu, J. / Liu, Q. / Xiang, Y.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31925023 China
National Natural Science Foundation of China (NSFC)21827810 China
National Natural Science Foundation of China (NSFC)31861143027 China
National Natural Science Foundation of China (NSFC)31470721 China
CitationJournal: To Be Published
Title: Structural insights into the HIV-1 Vpr mediated ubiquitination through the Cullin-RING E3 ubiquitin ligase
Authors: Wang, D. / Xu, J. / Liu, Q. / Xiang, Y.
History
DepositionAug 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DDB1- and CUL4-associated factor 1
B: DNA damage-binding protein 1
C: DDB1- and CUL4-associated factor 1
D: DNA damage-binding protein 1


Theoretical massNumber of molelcules
Total (without water)592,5854
Polymers592,5854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21850 Å2
ΔGint-92 kcal/mol
Surface area207470 Å2

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Components

#1: Protein DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 169194.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#2: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CryoEM structure of DDB1-VprBP complex in "ARM-up" conformation
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameCategory
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84405 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL

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