3G26 | pdb_00003g26

Crystal structure of the C-terminal domain of the Rous Sarcoma Virus capsid protein: Mutant A184C

• PDB DOI: https://doi.org/10.2210/pdb3G26/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Rous sarcoma virus - Prague C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-01-30 Released: 2009-06-02 
• Deposition Author(s): Kingston, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.214 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Proton-linked dimerization of a retroviral capsid protein initiates capsid assembly

Bailey, G.D., Hyun, J.K., Mitra, A.K., Kingston, R.L.

(2009) Structure 17: 737-748

• PubMed: 19446529 
• DOI: https://doi.org/10.1016/j.str.2009.03.010
• Primary Citation Related Structures: 
  3G0V, 3G1G, 3G1I, 3G21, 3G26, 3G28, 3G29


• PubMed Abstract: 
  

  In mature retroviral particles, the capsid protein (CA) forms a shell encasing the viral replication complex. Human immunodeficiency virus (HIV) CA dimerizes in solution, through its C-terminal domain (CTD), and this interaction is important for capsid assembly. In contrast, other retroviral capsid proteins, including that of Rous sarcoma virus (RSV), do not dimerize with measurable affinity. Here we show, using X-ray crystallography and other biophysical methods, that acidification causes RSV CA to dimerize in a fashion analogous to HIV CA, and that this drives capsid assembly in vitro. A pair of aspartic acid residues, located within the CTD dimer interface, explains why dimerization is linked to proton binding. Our results show that despite overarching structural similarities, the intermolecular forces responsible for forming and stabilizing the retroviral capsid differ markedly across retroviral genera. Our data further suggest that proton binding may regulate RSV capsid assembly, or modulate stability of the assembled capsid.

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Organizational Affiliation: 
• School of Biological Sciences, University of Auckland, Auckland, New Zealand.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 8.61 kDa 
• Atom Count: 719 
• Modeled Residue Count: 77 
• Deposited Residue Count: 77 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	A	77	Rous sarcoma virus - Prague C	Mutation(s): 1  Gene Names: gag EC: 3.4.23
UniProt
Find proteins for P03322 (Rous sarcoma virus subgroup C (strain Prague)) Explore P03322  Go to UniProtKB:  P03322

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA	B [auth A]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.214 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.243	α = 90
b = 32.243	β = 90
c = 113.993	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): Kingston, R.L.

Revision History  

• Version 1.0: 2009-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2015-04-29
  Changes: Non-polymer description
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.4: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary