8TVC | pdb_00008tvc

Crystal structure of rA3G-ssDNA-AA

• PDB DOI: https://doi.org/10.2210/pdb8TVC/pdb
• NAKB: 8TVC

• Classification: HYDROLASE/DNA
• Organism(s): Macaca mulatta, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-18 Released: 2024-11-06 
• Deposition Author(s): Yang, H., Pacheco, J.I., Chen, X.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.208 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain.

Yang, H., Pacheco, J., Kim, K., Bokani, A., Ito, F., Ebrahimi, D., Chen, X.S.

(2024) Nat Commun 15: 8773-8773

• PubMed: 39389938 
• DOI: https://doi.org/10.1038/s41467-024-52671-1
• Primary Citation Related Structures: 
  8TVC, 8TX4


• PubMed Abstract: 
  

  APOBEC3G, part of the AID/APOBEC cytidine deaminase family, is crucial for antiviral immunity. It has two zinc-coordinated cytidine-deaminase domains. The non-catalytic N-terminal domain strongly binds to nucleic acids, whereas the C-terminal domain catalyzes C-to-U editing in single-stranded DNA. The interplay between the two domains is not fully understood. Here, we show that DNA editing function of rhesus macaque APOBEC3G on linear and hairpin loop DNA is enhanced by AA or GA dinucleotide motifs present downstream in the 3'-direction of the target-C editing sites. The effective distance between AA/GA and the target-C sites is contingent on the local DNA secondary structure. We present two co-crystal structures of rhesus macaque APOBEC3G bound to ssDNA containing AA and GA, revealing the contribution of the non-catalytic domain in capturing AA/GA DNA. Our findings elucidate the molecular mechanism of APOBEC3G's cooperative function, which is critical for its antiviral role and its contribution to mutations in cancer genomes.

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Organizational Affiliation: 
• Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
School of Engineering and Technology, CQUniversity, Sydney, NSW, 2000, Australia.
Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA, 90095, USA.
California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
Molecular and Computational Biology, Departments of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA. [e-mail].
Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, Los Angeles, CA, 90033, USA. [e-mail].
Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA. [e-mail].
Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.8 kDa 
• Atom Count: 3,470 
• Modeled Residue Count: 379 
• Deposited Residue Count: 407 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA dC->dU-editing enzyme APOBEC-3G	A	386	Macaca mulatta	Mutation(s): 0  Gene Names: APOBEC3G EC: 3.5.4 (PDB Primary Data), 3.5.4.38 (UniProt)
UniProt
Find proteins for Q7YR23 (Macaca mulatta) Explore Q7YR23  Go to UniProtKB:  Q7YR23

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA 21-mer	B	21	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.208 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.429	α = 90
b = 68.461	β = 90
c = 126.735	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
JBluIce-EPICS	data collection
PHASER	phasing
xia2	data scaling
xia2	data reduction
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Yang, H., Pacheco, J.I., Chen, X.S.

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

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release