7V7C

CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex

• PDB DOI: https://doi.org/10.2210/pdb7V7C/pdb
• EM Map EMD-31766: EMDB EMDataResource

• Classification: TRANSFERASE/DNA BINDING PROTEIN/VIRAL PROTEIN
• Organism(s): Homo sapiens, Human immunodeficiency virus 1
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-21 Released: 2022-08-31 
• Deposition Author(s): Wang, D., Xu, J., Liu, Q., Xiang, Y.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into the HIV-1 Vpr mediated ubiquitination through the Cullin-RING E3 ubiquitin ligase

Wang, D., Xu, J., Liu, Q., Xiang, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 665.65 kDa 
• Atom Count: 40,264 
• Modelled Residue Count: 5,084 
• Deposited Residue Count: 5,926 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 1	A, E	1,507	Homo sapiens	Mutation(s): 0  Gene Names: DCAF1, KIAA0800, RIP, VPRBP EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4B6 (Homo sapiens) Explore Q9Y4B6  Go to UniProtKB:  Q9Y4B6
PHAROS:  Q9Y4B6 GTEx:  ENSG00000145041

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	B, F	1,140	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Vpr	C, G	96	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: vpr
UniProt
Find proteins for P12520 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12520  Go to UniProtKB:  P12520

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	D, H	220	Homo sapiens	Mutation(s): 0  Gene Names: UNG, DGU, UNG1, UNG15 EC: 3.2.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P13051 (Homo sapiens) Explore P13051  Go to UniProtKB:  P13051
PHAROS:  P13051 GTEx:  ENSG00000076248

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-31 
Deposition Author(s): Wang, D., Xu, J., Liu, Q., Xiang, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0501100
National Natural Science Foundation of China (NSFC)	China	31925023
National Natural Science Foundation of China (NSFC)	China	21827810
National Natural Science Foundation of China (NSFC)	China	31861143027
National Natural Science Foundation of China (NSFC)	China	31470721

Revision History  

• Version 1.0: 2022-08-31
  Type: Initial release