4V4M

1.45 Angstrom Structure of STNV coat protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 Biol 413: 41-50

  • DOI: 10.1016/j.jmb.2011.07.062
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • 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