4Y5Z

T=1 capsid structure of SeMV Ndel65CP fused with B-domain of S. aureus protein SpA at the N-terminus (P1 crystal form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural studies on chimeric Sesbania mosaic virus coat protein: Revisiting SeMV assembly.

Gulati, A.Murthy, A.Abraham, A.Mohan, K.Natraj, U.Savithri, H.S.Murthy, M.R.

(2015) Virology 489: 34-43

  • DOI: https://doi.org/10.1016/j.virol.2015.11.029
  • Primary Citation of Related Structures:  
    4Y4Y, 4Y5Z

  • PubMed Abstract: 

    The capsid protein (CP) of Sesbania mosaic virus (SeMV, a T=3 plant virus) consists of a disordered N-terminal R-domain and an ordered S-domain. Removal of the R-domain results in the formation of T=1 particles. In the current study, the R-domain was replaced with unrelated polypeptides of similar lengths: the B-domain of Staphylococcus aureus SpA, and SeMV encoded polypeptides P8 and P10. The chimeric proteins contained T=3 or larger virus-like particles (VLPs) and could not be crystallized. The presence of metal ions during purification resulted in a large number of heterogeneous nucleoprotein complexes. N∆65-B (R domain replaced with B domain) could also be purified in a dimeric form. Its crystal structure revealed T=1 particles devoid of metal ions and the B-domain was disordered. However, the B-domain was functional in N∆65-B VLPs, suggesting possible biotechnological applications. These studies illustrate the importance of N-terminal residues, metal ions and robustness of the assembly process.


  • Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoglobulin G-binding protein A,Coat protein282Staphylococcus aureus subsp. aureus NCTC 8325Sesbania mosaic virus
This entity is chimeric
Mutation(s): 0 
Gene Names: spaSAOUHSC_00069
UniProt
Find proteins for Q9EB06 (Sesbania mosaic virus)
Explore Q9EB06 
Go to UniProtKB:  Q9EB06
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P02976 
Go to UniProtKB:  P02976
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP02976Q9EB06
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
IB [auth A]
JB [auth H]
KB [auth M]
LB [auth P]
MB [auth X]
IB [auth A],
JB [auth H],
KB [auth M],
LB [auth P],
MB [auth X],
NB [auth Z],
OB [auth o],
PB [auth s],
QB [auth w],
RB [auth 4],
SB [auth 7],
TB [auth h]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.48α = 61.09
b = 187.42β = 89.24
c = 187.93γ = 60.2
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DST, DBT, J.C BoseIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-11-29
    Changes: Database references