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Open data
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Basic information
Entry | Database: PDB / ID: 5jk7 | ||||||
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Title | The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex | ||||||
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![]() | Viral protein/DNA BINDING PROTEIN / Cullin4-RING E3 ubiquitin ligase HIV-1 Vpr UNG2 / DNA BINDING PROTEIN-HYDROLASE complex / Viral protein-DNA BINDING PROTEIN complex | ||||||
Function / homology | ![]() histone H2AT120 kinase activity / cell competition in a multicellular organism / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / epigenetic programming in the zygotic pronuclei ...histone H2AT120 kinase activity / cell competition in a multicellular organism / symbiont-mediated arrest of host cell cycle during G2/M transition / base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / positive regulation by virus of viral protein levels in host cell / V(D)J recombination / epigenetic programming in the zygotic pronuclei / isotype switching / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / uracil DNA N-glycosylase activity / 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 / ribosomal small subunit binding / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / somatic hypermutation of immunoglobulin genes / monoatomic ion transmembrane transport / positive regulation of gluconeogenesis / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / B cell differentiation / post-translational protein modification / Chromatin modifications during the maternal to zygotic transition (MZT) / virion component / nuclear estrogen receptor binding / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / base-excision repair / protein homooligomerization / 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 / viral penetration into host nucleus / positive regulation of protein catabolic process / cellular response to UV / host cell / 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 / host extracellular space / chromosome, telomeric region / damaged DNA binding / non-specific serine/threonine protein kinase / protein ubiquitination / symbiont entry into host cell / cell cycle / phosphorylation / DNA repair / protein serine kinase activity / DNA-templated transcription / apoptotic process / DNA damage response / host cell nucleus / protein-containing complex binding / regulation of DNA-templated transcription / nucleolus / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / extracellular space / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Calero, G. / Ahn, J. / Wu, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction. Authors: Wu, Y. / Zhou, X. / Barnes, C.O. / DeLucia, M. / Cohen, A.E. / Gronenborn, A.M. / Ahn, J. / Calero, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 518.8 KB | Display | ![]() |
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Full document | ![]() | 638.4 KB | Display | |
Data in XML | ![]() | 123.9 KB | Display | |
Data in CIF | ![]() | 166 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 127097.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q16531 #2: Protein | Mass: 41178.234 Da / Num. of mol.: 2 / Fragment: UNP residues 1045-1396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase #3: Protein | Mass: 25382.957 Da / Num. of mol.: 2 / Fragment: UNP residues 85-304 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: P13051, uracil-DNA glycosylase #4: Protein | Mass: 11396.878 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: isolate NY5 / Gene: vpr Production host: ![]() References: UniProt: P12520 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.91 % |
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Crystal grow | Temperature: 289.15 K / Method: batch mode / Details: 100 mM Na Ctrate, pH 5.6, 11% PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.49→40.3 Å / Num. obs: 77315 / Biso Wilson estimate: 188.78 Å2 |
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Processing
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Refinement | Resolution: 3.49→40.3 Å / Cor.coef. Fo:Fc: 0.9415 / Cor.coef. Fo:Fc free: 0.9297 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.422
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Displacement parameters | Biso mean: 193.89 Å2
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Refine analyze | Luzzati coordinate error obs: 1.036 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.49→40.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.49→3.58 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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