8CX2

Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structural basis for HIV-1 Vif antagonism of human APOBEC3G.

Li, Y.L.Langley, C.A.Azumaya, C.M.Echeverria, I.Chesarino, N.M.Emerman, M.Cheng, Y.Gross, J.D.

(2023) Nature 615: 728-733

  • DOI: https://doi.org/10.1038/s41586-023-05779-1
  • Primary Citation of Related Structures:  
    8CX0, 8CX1, 8CX2

  • PubMed Abstract: 

    The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles 1-4 . The lentiviruses encode a protein, Vif, that antagonizes A3 family members by targeting them for degradation. Diversification of A3 allows host escape from Vif whereas adaptations in Vif enable cross-species transmission of primate lentiviruses. How this 'molecular arms race' plays out at the structural level is unknown. Here, we report the cryogenic electron microscopy structure of human APOBEC3G (A3G) bound to HIV-1 Vif, and the hijacked cellular proteins that promote ubiquitin-mediated proteolysis. A small surface explains the molecular arms race, including a cross-species transmission event that led to the birth of HIV-1. Unexpectedly, we find that RNA is a molecular glue for the Vif-A3G interaction, enabling Vif to repress A3G by ubiquitin-dependent and -independent mechanisms. Our results suggest a model in which Vif antagonizes A3G by intercepting it in its most dangerous form for the virus-when bound to RNA and on the pathway to packaging-to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism by which RNA binding helps to position key residues necessary for viral antagonism of a host antiviral gene.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA dC->dU-editing enzyme APOBEC-3G
A, F
421Homo sapiensMutation(s): 0 
Gene Names: APOBEC3GMDS019
EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC16 (Homo sapiens)
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Go to UniProtKB:  Q9HC16
PHAROS:  Q9HC16
GTEx:  ENSG00000239713 
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UniProt GroupQ9HC16
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Virion infectivity factor
B, G
192Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: vif
UniProt
Find proteins for P69723 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
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Go to UniProtKB:  P69723
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UniProt GroupP69723
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Core-binding factor subunit beta
C, H
182Homo sapiensMutation(s): 0 
Gene Names: CBFB
UniProt & NIH Common Fund Data Resources
Find proteins for Q13951 (Homo sapiens)
Explore Q13951 
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PHAROS:  Q13951
GTEx:  ENSG00000067955 
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UniProt GroupQ13951
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-B
D, I
118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
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PHAROS:  Q15370
GTEx:  ENSG00000103363 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-C
E, J
112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Find proteins for Q15369 (Homo sapiens)
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PHAROS:  Q15369
GTEx:  ENSG00000154582 
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*AP*UP*AP*AP*AP*AP*AP*U)-3')9Spodoptera frugiperda
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*UP*AP*AP*AP*AP*AP*U)-3')9Spodoptera frugiperda
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCV3.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI150476

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release
  • Version 1.1: 2023-02-22
    Changes: Database references
  • Version 1.2: 2023-04-05
    Changes: Database references
  • Version 1.3: 2024-06-12
    Changes: Data collection