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 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report



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:  
    6P3X, 6P40, 6P3Z, 6P3Y

  • 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

    Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA, 90089, USA. xiaojiac@usc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apolipoprotein B mRNA editing enzyme, catalytic peptide-like 3GAB386Macaca mulattaMutation(s): 0 
Gene Names: APOBEC3G
EC: 3.5.4
Find proteins for M1GSK9 (Macaca mulatta)
Explore M1GSK9 
Go to UniProtKB:  M1GSK9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.695α = 90
b = 153.849β = 116.37
c = 67.728γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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