Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 245.62 kDa 
• Atom Count: 15,041 
• Modelled Residue Count: 1,774 
• Deposited Residue Count: 2,068 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

 8CX2

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

• PDB DOI:  https://doi.org/10.2210/pdb8CX2/pdb
• EM Map EMD-27034: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM/RNA
• Organism(s): Homo sapiens, Human immunodeficiency virus 1, Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-05-19 Released: 2023-02-15 
• Deposition Author(s): Li, Y., Langley, C., Azumaya, C.M., Echeverria, I., Chesarino, N.M., Emerman, M., Cheng, Y., Gross, J.D.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

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

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

• PubMed: 36754086 
• 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 APOBE3G (A3G) bound to HIV-1 Vif and 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 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 where Vif antagonizes A3G by intercepting it in its most dangerous form for the virus, when bound to RNA and on pathway to packaging, to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism where RNA binding helps position key residues necessary for viral antagonism of a host antiviral gene.

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Organizational Affiliation: 

Quantitative Bioscience Institute, University of California, San Francisco, San Francisco, CA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA dC->dU-editing enzyme APOBEC-3G	A, F	421	Homo sapiens	Mutation(s): 0  Gene Names: APOBEC3G, MDS019 EC: 3.5.4.38
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC16 (Homo sapiens) Explore Q9HC16  Go to UniProtKB:  Q9HC16
PHAROS:  Q9HC16

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion infectivity factor	B, G	192	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: vif
UniProt
Find proteins for Q77YG0 (Human immunodeficiency virus 1) Explore Q77YG0  Go to UniProtKB:  Q77YG0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Core-binding factor subunit beta	C, H	182	Homo sapiens	Mutation(s): 0  Gene Names: CBFB
UniProt & NIH Common Fund Data Resources
Find proteins for Q13951 (Homo sapiens) Explore Q13951  Go to UniProtKB:  Q13951
PHAROS:  Q13951

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	D, I	118	Homo sapiens	Mutation(s): 0  Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370  Go to UniProtKB:  Q15370
PHAROS:  Q15370

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	E, J	112	Homo sapiens	Mutation(s): 0  Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369  Go to UniProtKB:  Q15369
PHAROS:  Q15369

Entity ID: 6
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*UP*AP*AP*AP*AP*AP*U)-3')	K	9	Spodoptera frugiperda

Entity ID: 7
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*UP*AP*AP*AP*AP*AP*U)-3')	L	9	Spodoptera frugiperda

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	M [auth A], N [auth A], O [auth B], P [auth F], Q [auth F], R [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	V3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Li, Y., Langley, C., Azumaya, C.M., Echeverria, I., Chesarino, N.M., Emerman, M., Cheng, Y., Gross, J.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI150476

Revision History  

• 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