1ZA7 | pdb_00001za7

The crystal structure of salt stable cowpea cholorotic mottle virus at 2.7 angstroms resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 
    0.245 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 
    0.245 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Enhanced local symmetry interactions globally stabilize a mutant virus capsid that maintains infectivity and capsid dynamics.

Speir, J.A.Bothner, B.Qu, C.Willits, D.A.Young, M.J.Johnson, J.E.

(2006) J Virol 80: 3582-3591

  • DOI: https://doi.org/10.1128/JVI.80.7.3582-3591.2006
  • Primary Citation Related Structures: 
    1ZA7

  • PubMed Abstract: 

    Structural transitions in viral capsids play a critical role in the virus life cycle, including assembly, disassembly, and release of the packaged nucleic acid. Cowpea chlorotic mottle virus (CCMV) undergoes a well-studied reversible structural expansion in vitro in which the capsid expands by 10%. The swollen form of the particle can be completely disassembled by increasing the salt concentration to 1 M. Remarkably, a single-residue mutant of the CCMV N-terminal arm, K42R, is not susceptible to dissociation in high salt (salt-stable CCMV [SS-CCMV]) and retains 70% of wild-type infectivity. We present the combined structural and biophysical basis for the chemical stability and viability of the SS-CCMV particles. A 2.7-A resolution crystal structure of the SS-CCMV capsid shows an addition of 660 new intersubunit interactions per particle at the center of the 20 hexameric capsomeres, which are a direct result of the K42R mutation. Protease-based mapping experiments of intact particles demonstrate that both the swollen and closed forms of the wild-type and SS-CCMV particles have highly dynamic N-terminal regions, yet the SS-CCMV particles are more resistant to degradation. Thus, the increase in SS-CCMV particle stability is a result of concentrated tethering of subunits at a local symmetry interface (i.e., quasi-sixfold axes) that does not interfere with the function of other key symmetry interfaces (i.e., fivefold, twofold, quasi-threefold axes). The result is a particle that is still dynamic but insensitive to high salt due to a new series of bonds that are resistant to high ionic strength and preserve the overall particle structure.


  • Organizational Affiliation
    • Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 52.8 kDa 
  • Atom Count: 3,741 
  • Modeled Residue Count: 481 
  • Deposited Residue Count: 495 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coat protein
A, B, C
165Cowpea chlorotic mottle virusMutation(s): 2 
Gene Names: RNA4
UniProt
Find proteins for P03601 (Cowpea chlorotic mottle virus)
Explore P03601 
Go to UniProtKB:  P03601
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03601
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work:  0.245 (Depositor), 0.243 (DCC) 
  • R-Value Observed: 0.245 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 365.48α = 90
b = 374.86β = 90
c = 402.49γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
GLRFphasing
RAVEphasing
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references
  • Version 1.5: 2023-08-23
    Changes: Data collection, Derived calculations, Refinement description