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Open data
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Basic information
Entry | Database: PDB / ID: 7v7b | ||||||||||||||||||
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Title | CryoEM structure of DDB1-VprBP complex in ARM-up conformation | ||||||||||||||||||
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![]() | TRANSFERASE/DNA BINDING PROTEIN / Ubiquitin pathway / E3 ligase / Substrate recognition unit / LIGASE / TRANSFERASE-DNA BINDING PROTEIN complex | ||||||||||||||||||
Function / homology | ![]() histone H2AT120 kinase activity / cell competition in a multicellular organism / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / 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 / WD40-repeat domain binding ...histone H2AT120 kinase activity / cell competition in a multicellular organism / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / 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 / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / 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 / cullin family protein binding / viral release from host cell / ubiquitin-like ligase-substrate adaptor activity / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / positive regulation of gluconeogenesis / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / damaged DNA binding / non-specific serine/threonine protein kinase / protein ubiquitination / phosphorylation / DNA repair / protein serine kinase activity / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||
![]() | Wang, D. / Xu, J. / Liu, Q. / Xiang, Y. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 781.2 KB | Display | ![]() |
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PDB format | ![]() | 635.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 943.5 KB | Display | ![]() |
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Full document | ![]() | 978.4 KB | Display | |
Data in XML | ![]() | 111.9 KB | Display | |
Data in CIF | ![]() | 170.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 31765MC ![]() 7v7cC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 169194.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase #2: Protein | Mass: 127097.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: CryoEM structure of DDB1-VprBP complex in "ARM-up" conformation Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | |||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84405 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |