7M3T

Crystallographic structure of a cubic crystal of STMV (80.7 degree rotation about 111) grown from chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.

McPherson, A.

(2021) Acta Crystallogr F Struct Biol Commun 77: 473-483

  • DOI: 10.1107/S2053230X21011547
  • Primary Citation of Related Structures:  
    5BKL, 5BKN, 5BKQ, 7M2T, 7M2V, 7M3R, 7M3T, 7M50, 7M54, 7M57

  • PubMed Abstract: 
  • The structures of new crystal forms of Satellite tobacco mosaic virus (STMV) are described. These belong to space groups I2, P2 1 2 1 2 (a low-resolution form), R3 (H3) and P23. The R3 crystals are 50%/50% twinned, as are two instances of the P23 crystals ...

    The structures of new crystal forms of Satellite tobacco mosaic virus (STMV) are described. These belong to space groups I2, P2 1 2 1 2 (a low-resolution form), R3 (H3) and P23. The R3 crystals are 50%/50% twinned, as are two instances of the P23 crystals. The I2 and P2 1 2 1 2 crystals were grown from ammonium sulfate solutions, as was one crystal in space group P23, while the R3 and the other P23 crystals were grown from sodium chloride, sodium bromide and sodium nitrate. The monoclinic and orthorhombic crystals have half a virus particle as the asymmetric unit, while the rhombohedral and cubic crystals have one third of a virus particle. RNA segments organized about the icosahedral twofold axes were present in crystals grown from ammonium sulfate and sodium chloride, as in the canonical I222 crystals (PDB entry 4oq8), but were not observed in crystals grown from sodium bromide and sodium nitrate. Bromide and nitrate ions generally replaced the RNA phosphates present in the I222 crystals, including the phosphates seen on fivefold axes, and were also found at threefold vertices in both the rhombohedral and cubic forms. An additional anion was also found on the fivefold axis 5 Å from the first anion, and slightly outside the capsid in crystals grown from sodium chloride, sodium bromide and sodium nitrate, suggesting that the path along the symmetry axis might be an ion channel. The electron densities for RNA strands at individual icosahedral dyads, as well as at the amino-terminal peptides of protein subunits, exhibited a diversity of orientations, in particular the residues at the ends.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, University of California, 530A Steinhaus Hall, Irvine, CA 92697-3900, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein
A,
B,
C,
D,
E,
159Satellite tobacco mosaic virusMutation(s): 0 
UniProt
Find proteins for P17574 (Satellite tobacco mosaic virus)
Explore P17574 
Go to UniProtKB:  P17574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17574
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coat proteinG159Satellite tobacco mosaic virusMutation(s): 0 
UniProt
Find proteins for P17574 (Satellite tobacco mosaic virus)
Explore P17574 
Go to UniProtKB:  P17574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17574
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Coat proteinN159Satellite tobacco mosaic virusMutation(s): 0 
UniProt
Find proteins for P17574 (Satellite tobacco mosaic virus)
Explore P17574 
Go to UniProtKB:  P17574
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17574
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')10Satellite tobacco mosaic virus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')IA [auth WW],
W [auth e]
12Satellite tobacco mosaic virus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 6
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')X [auth h]12Satellite tobacco mosaic virus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 7
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')Y [auth i],
LA [auth ll]
11Satellite tobacco mosaic virus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 8
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')KA [auth kk],
Z [auth m]
10Satellite tobacco mosaic virus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 9
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')AA [auth n],
MA [auth qq]
8Satellite tobacco mosaic virus
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 10
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')JA [auth bb]12Satellite tobacco mosaic virus
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
BB [auth GG],
MB [auth ll],
NA [auth A],
SA [auth H],
UA [auth H],
BB [auth GG],
MB [auth ll],
NA [auth A],
SA [auth H],
UA [auth H],
VA [auth L],
ZA [auth S]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
AB [auth T],
CB [auth HH],
GB [auth JJ],
HB [auth KK],
IB [auth KK],
AB [auth T],
CB [auth HH],
GB [auth JJ],
HB [auth KK],
IB [auth KK],
JB [auth bb],
KB [auth bb],
LB [auth bb],
NB [auth qq],
OA [auth C],
OB [auth U],
PA [auth D],
RA [auth G],
XA [auth M],
YA [auth N]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DB [auth II],
EB [auth JJ],
FB [auth JJ],
QA [auth G],
TA [auth H],
DB [auth II],
EB [auth JJ],
FB [auth JJ],
QA [auth G],
TA [auth H],
WA [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.05α = 90
b = 234.05β = 90
c = 234.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references