4OQ9 | pdb_00004oq9

Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry restraints

• PDB DOI: https://doi.org/10.2210/pdb4OQ9/pdb
• NAKB: 4OQ9

• Classification: VIRUS/RNA
• Organism(s): Satellite tobacco mosaic virus
• Mutation(s): No 


• Deposited: 2014-02-07 Released: 2014-09-10 
• Deposition Author(s): Larson, S.B., Day, J.S., McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.250 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Satellite tobacco mosaic virus refined to 1.4 angstrom resolution.

Larson, S.B., Day, J.S., McPherson, A.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2316-2330

• PubMed: 25195746 
• DOI: https://doi.org/10.1107/S1399004714013789
• Primary Citation Related Structures: 
  4NIA, 4OQ8, 4OQ9


• PubMed Abstract: 
  

  Satellite tobacco mosaic virus (STMV) is among the smallest viruses, having 60 identical subunits arranged with T = 1 icosahedral symmetry. Its crystal structure was solved at 290 K and was refined using, in part, crystals grown in microgravity. Electron-density maps revealed nearly 57% of the genomic ssRNA. Using six flash-cooled crystals, diffraction data were recorded to 1.4 Å resolution and independent refinements of the STMV model were carried out versus the previous 1.8 Å resolution data representing merged data from 21 crystals (271,689 unique reflections), data consisting of corresponding reflections to 1.8 Å resolution from the cooled crystals and 1.4 Å resolution data from the cooled crystals comprised of 570,721 unique reflections. Models were independently refined with full NCS constraints using the program CNS and in restrained mode using the programs CNS, REFMAC5 and SHELX-97, with the latter two procedures including anisotropic temperature factors. Significant additional structural detail emerged from the analyses, including a unique cation and anion arrangement on fivefold axes and a precise assessment of icosahedral symmetry exactness in the crystal lattice. STMV represents the highest resolution native virus structure currently known by a substantial margin, and it permits the evaluation of a precise atomic model of a spherical virus at near-atomic resolution for the first time.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 367.95 kDa 
• Atom Count: 29,296 
• Modeled Residue Count: 2,490 
• Deposited Residue Count: 2,715 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	159	Satellite tobacco mosaic virus	Mutation(s): 0
UniProt
Find proteins for P17574 (Satellite tobacco mosaic virus) Explore P17574  Go to UniProtKB:  P17574

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')	AA [auth a], BA [auth b], CA [auth c], DA [auth d], P, Q, R, S, T, U, V, W, X, Y, Z	10	Satellite tobacco mosaic virus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')	EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s]	10	Satellite tobacco mosaic virus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*UP*U)-3')	AB [auth 1], BB [auth 2], CB [auth 3], DB [auth 4], EB [auth 5], FB [auth 6], GB [auth 7], HB [auth 8], TA [auth t], UA [auth u], VA [auth v], WA [auth w], XA [auth x], YA [auth y], ZA [auth z]	2	Satellite tobacco mosaic virus

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AC [auth G], BC [auth G], EC [auth H], GC [auth I], IC [auth J], JB [auth A], KC [auth K], LB [auth B], NC [auth L], OB [auth C], PC [auth M], QB [auth D], QC [auth M], SB [auth E], TB [auth E], TC [auth N], VC [auth O], XB [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	DC [auth H], IB [auth A], SC [auth N]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	LC [auth K], UB [auth E], YB [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	CC [auth G], FC [auth H], HC [auth I], JC [auth J], KB [auth A], MB [auth B], MC [auth K], NB [auth B], OC [auth L], PB [auth C], RB [auth D], RC [auth M], UC [auth N], VB [auth E], WB [auth E], WC [auth O], ZB [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.250 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.69	α = 90
b = 190.3	β = 90
c = 201.69	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
Coot	model building
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Larson, S.B., Day, J.S., McPherson, A.

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description