4V4M | pdb_00004v4m

1.45 Angstrom Structure of STNV coat protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.208 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4V4M

This is version 1.2 of the entry. See complete history

Literature

Construction and crystal structure of recombinant STNV capsids.

Lane, S.W.Dennis, C.A.Lane, C.L.Trinh, C.H.Rizkallah, P.J.Stockley, P.G.Phillips, S.E.

(2011) J Mol Biology 413: 41-50

  • DOI: https://doi.org/10.1016/j.jmb.2011.07.062
  • Primary Citation Related Structures: 
    3S4G, 4V4M

  • PubMed Abstract: 

    A codon-optimised gene has been expressed in Escherichia coli to produce the coat protein (CP) of the Satellite Tobacco Necrosis Virus. This protein assembles in vivo into capsids closely resembling those of the T=1 wild-type virus. These virus-like particles (VLPs) package the recombinant mRNA transcript and can be disassembled and reassembled using different buffer conditions. The X-ray crystal structure of the VLP has been solved and refined at 1.4 Å resolution and shown to be very similar to that of wild-type Satellite Tobacco Necrosis Virus, except that icosahedral symmetry constraints could be removed to reveal differences between subunits, presumably owing to crystal packing. An additional low-resolution X-ray crystal structure determination revealed well-ordered RNA fragments lodged near the inside surface of the capsid, close to basic clusters formed by the N-terminal helices that project into the interior of the particle. The RNA consists of multiple copies of a 3-bp helical stem, with a single unpaired base at the 3' end, and probably consists of a number of short stem-loops where the loop region is disordered. The arrangement of the RNA is different from that observed in other satellite viruses.


  • Organizational Affiliation
    • Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

Macromolecule Content 

  • Total Structure Weight: 1,308.07 kDa 
  • Atom Count: 102,135 
  • Modeled Residue Count: 11,040 
  • Deposited Residue Count: 11,760 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coat protein196Satellite tobacco necrosis virus 1Mutation(s): 0 
UniProt
Find proteins for P03606 (Satellite tobacco necrosis virus 1)
Explore P03606 
Go to UniProtKB:  P03606
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03606
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
AC [auth r]
AD [auth A]
AE [auth Q]
BC [auth s]
BD [auth B]
AC [auth r],
AD [auth A],
AE [auth Q],
BC [auth s],
BD [auth B],
BE [auth R],
CC [auth t],
CD [auth B],
CE [auth R],
DC [auth u],
DD [auth B],
DE [auth S],
EC [auth v],
ED [auth C],
EE [auth S],
FC [auth w],
FD [auth D],
FE [auth T],
GC [auth x],
GD [auth E],
GE [auth T],
HC [auth y],
HD [auth E],
HE [auth U],
IB [auth e],
IC [auth z],
ID [auth E],
IE [auth U],
JB [auth f],
JC [auth 0],
JD [auth F],
JE [auth U],
KB [auth g],
KC [auth 0],
KD [auth G],
KE [auth V],
LB [auth h],
LC [auth 1],
LD [auth G],
LE [auth V],
MB [auth i],
MC [auth 1],
MD [auth G],
ME [auth W],
NB [auth i],
NC [auth 1],
ND [auth H],
NE [auth X],
OB [auth j],
OC [auth 2],
OD [auth I],
OE [auth Y],
PB [auth j],
PC [auth 2],
PD [auth I],
PE [auth Z],
QB [auth k],
QC [auth 3],
QD [auth J],
QE [auth a],
RB [auth l],
RC [auth 3],
RD [auth K],
RE [auth b],
SB [auth m],
SC [auth 4],
SD [auth K],
SE [auth b],
TB [auth n],
TC [auth 4],
TD [auth L],
TE [auth c],
UB [auth n],
UC [auth 5],
UD [auth M],
UE [auth c],
VB [auth o],
VC [auth 5],
VD [auth N],
VE [auth d],
WB [auth o],
WC [auth 6],
WD [auth N],
XB [auth p],
XC [auth 6],
XD [auth O],
YB [auth q],
YC [auth 7],
YD [auth P],
ZB [auth q],
ZC [auth A],
ZD [auth Q]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 307.585α = 90
b = 302.265β = 92.77
c = 181.923γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description