8J62 | pdb_00008j62

Cryo-EM structure of APOBEC3G-Vif complex

• PDB DOI: https://doi.org/10.2210/pdb8J62/pdb
• NAKB: 8J62
• EM Map EMD-35999: EMDB EMDataResource

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Homo sapiens, Human immunodeficiency virus 1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-24 Released: 2023-07-19 
• Deposition Author(s): Kouno, T., Shibata, S., Hyun, J., Kim, T.G., Wolf, M.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural insights into RNA bridging between HIV-1 Vif and antiviral factor APOBEC3G.

Kouno, T., Shibata, S., Shigematsu, M., Hyun, J., Kim, T.G., Matsuo, H., Wolf, M.

(2023) Nat Commun 14: 4037-4037

• PubMed: 37419875 
• DOI: https://doi.org/10.1038/s41467-023-39796-5
• Primary Citation Related Structures: 
  8H0I, 8J62


• PubMed Abstract: 
  

  Great effort has been devoted to discovering the basis of A3G-Vif interaction, the key event of HIV's counteraction mechanism to evade antiviral innate immune response. Here we show reconstitution of the A3G-Vif complex and subsequent A3G ubiquitination in vitro and report the cryo-EM structure of the A3G-Vif complex at 2.8 Å resolution using solubility-enhanced variants of A3G and Vif. We present an atomic model of the A3G-Vif interface, which assembles via known amino acid determinants. This assembly is not achieved by protein-protein interaction alone, but also involves RNA. The cryo-EM structure and in vitro ubiquitination assays identify an adenine/guanine base preference for the interaction and a unique Vif-ribose contact. This establishes the biological significance of an RNA ligand. Further assessment of interactions between A3G, Vif, and RNA ligands show that the A3G-Vif assembly and subsequent ubiquitination can be controlled by amino acid mutations at the interface or by polynucleotide modification, suggesting that a specific chemical moiety would be a promising pharmacophore to inhibit the A3G-Vif interaction.

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Organizational Affiliation: 
• Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan. [e-mail].
Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
Division of Bacteriology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago-shi, Tottori, 683-8503, Japan.
Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA.
School of Pharmacy, Sungkyunkwan University, Suwon-si, Gyeonggi-do, 16419, Republic of Korea.
Department of Efficacy Evaluation, Innovation Center for Vaccine Industry, Gyeongbuk Institute for Bio Industry, Gyeongsanbuk-do, 36618, Republic of Korea.
Cancer Innovation Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan. [e-mail].
Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, 115, Taipei, Taiwan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A4B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 10-mer - A4B4C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, microscopy

Macromolecule Content 

• Total Structure Weight: 247.42 kDa 
• Atom Count: 10,448 
• Modeled Residue Count: 1,220 
• Deposited Residue Count: 2,006 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
APOBEC3G	A, G [auth B]	371	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000239713

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Viral infectivity factor	B [auth C], D [auth E], H [auth G], J [auth I]	150	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P12504 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12504  Go to UniProtKB:  P12504

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Core binding factor beta	C [auth D], E [auth F], I [auth H], K [auth J]	156	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13951 (Homo sapiens) Explore Q13951  Go to UniProtKB:  Q13951
PHAROS:  Q13951 GTEx:  ENSG00000067955

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*GP*GP*UP*UP*GP*AP*UP*UP*GP*UP*UP*UP*UP*AP*AP*CP*AP*A)-3')	F [auth X], L [auth Y]	20	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	M [auth A], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.3
MODEL REFINEMENT	PHENIX	1.19.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Kouno, T., Shibata, S., Hyun, J., Kim, T.G., Wolf, M.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP18am0101076

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Data collection, Refinement description