6P3Y

Crystal Structure of Full Length APOBEC3G E/Q (pH 7.4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Understanding the structural basis of HIV-1 restriction by the full length double-domain APOBEC3G.

Yang, H.Ito, F.Wolfe, A.D.Li, S.Mohammadzadeh, N.Love, R.P.Yan, M.Zirkle, B.Gaba, A.Chelico, L.Chen, X.S.

(2020) Nat Commun 11: 632-632

  • DOI: 10.1038/s41467-020-14377-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • APOBEC3G, a member of the double-domain cytidine deaminase (CD) APOBEC, binds RNA to package into virions and restrict HIV-1 through deamination-dependent or deamination-independent inhibition. Mainly due to lack of a full-length double-domain APOBEC ...

    APOBEC3G, a member of the double-domain cytidine deaminase (CD) APOBEC, binds RNA to package into virions and restrict HIV-1 through deamination-dependent or deamination-independent inhibition. Mainly due to lack of a full-length double-domain APOBEC structure, it is unknown how CD1/CD2 domains connect and how dimerization/multimerization is linked to RNA binding and virion packaging for HIV-1 restriction. We report rhesus macaque A3G structures that show different inter-domain packing through a short linker and refolding of CD2. The A3G dimer structure has a hydrophobic dimer-interface matching with that of the previously reported CD1 structure. A3G dimerization generates a surface with intensified positive electrostatic potentials (PEP) for RNA binding and dimer stabilization. Unexpectedly, mutating the PEP surface and the hydrophobic interface of A3G does not abolish virion packaging and HIV-1 restriction. The data support a model in which only one RNA-binding mode is critical for virion packaging and restriction of HIV-1 by A3G.


    Organizational Affiliation

    Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA. xiaojiac@usc.edu.,Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.,Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA.,School of Pharmacy, Jining Medical University, 276800, Rizhao, Shandong, China.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.,Molecular and Computational Biology, Departments of Biological Sciences, Chemistry, University of Southern California, Los Angeles, CA, 90089, USA. xiaojiac@usc.edu.,Molecular and Computational Biology, Departments of Biological Sciences, Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA. xiaojiac@usc.edu.,Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA. xiaojiac@usc.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3G
A, B
386Macaca mulattaMutation(s): 0 
Gene Names: APOBEC3G
Find proteins for M1GSK9 (Macaca mulatta)
Go to Gene View: APOBEC3G
Go to UniProtKB:  M1GSK9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.695α = 90.00
b = 153.849β = 116.37
c = 67.728γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087986

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release