4V4M

1.45 Angstrom Structure of STNV coat protein

• PDB DOI:  https://doi.org/10.2210/pdb4V4M/pdb
• Entry: 4V4M supersedes: 3RQV, 1VTZ

• Classification: VIRUS
• Organism(s): Satellite tobacco necrosis virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-28 Released: 2014-07-09 
• Deposition Author(s): Lane, S.W., Dennis, C.A., Lane, C.L., Trinh, C.H., Rizkallah, P.J., Stockley, P.G., Phillips, S.E.V.

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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 

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

• PubMed: 21839089 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A [auth e], AA [auth 4], AB [auth W], B [auth f], BA [auth 5], BB [auth X], C [auth g], CA [auth 6], CB [auth Y], D [auth h], DA [auth 7], DB [auth Z], E [auth i], EA [auth A], EB [auth a], F [auth j], FA [auth B], FB [auth b], G [auth k], GA [auth C], GB [auth c], H [auth l], HA [auth D], HB [auth d], I [auth m], IA [auth E], J [auth n], JA [auth F], K [auth o], KA [auth G], L [auth p], LA [auth H], M [auth q], MA [auth I], N [auth r], NA [auth J], O [auth s], OA [auth K], P [auth t], PA [auth L], Q [auth u], QA [auth M], R [auth v], RA [auth N], S [auth w], SA [auth O], T [auth x], TA [auth P], U [auth y], UA [auth Q], V [auth z], VA [auth R], W [auth 0], WA [auth S], X [auth 1], XA [auth T], Y [auth 2], YA [auth U], Z [auth 3], ZA [auth V]	196	Satellite tobacco necrosis virus 1	Mutation(s): 0
UniProt
Find proteins for P03606 (Satellite tobacco necrosis virus 1) Explore P03606  Go to UniProtKB:  P03606

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	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 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 307.585	α = 90
b = 302.265	β = 92.77
c = 181.923	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Lane, S.W., Dennis, C.A., Lane, C.L., Trinh, C.H., Rizkallah, P.J., Stockley, P.G., Phillips, S.E.V.
• This entry supersedes: 3RQV, 1VTZ

Revision History  

• 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