7M54

Crystallographic structure of a cubic crystal form of STMV grown from bromide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/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 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
MoleculeChains Sequence LengthOrganismDetailsImage
Coat protein159Satellite 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BR (Subject of Investigation/LOI)
Query on BR

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth D]
AC [auth F]
AD [auth H]
AE [auth L]
AA [auth A],
AB [auth D],
AC [auth F],
AD [auth H],
AE [auth L],
AG [auth II],
AH [auth KK],
BA [auth A],
BB [auth D],
BC [auth F],
BD [auth H],
BE [auth L],
BF [auth GG],
BG [auth II],
BH [auth KK],
CA [auth A],
CB [auth D],
CC [auth F],
CD [auth H],
CE [auth L],
CF [auth GG],
CG [auth II],
CH [auth KK],
DA [auth A],
DB [auth D],
DC [auth F],
DD [auth H],
DE [auth L],
DF [auth GG],
DG [auth II],
DH [auth KK],
EB [auth D],
EC [auth F],
ED [auth H],
EE [auth L],
EF [auth GG],
EG [auth II],
EH [auth KK],
FA [auth B],
FB [auth D],
FD [auth I],
FE [auth L],
FF [auth GG],
FG [auth II],
FH [auth KK],
GA [auth B],
GB [auth D],
GD [auth I],
GE [auth L],
GF [auth GG],
GG [auth II],
GH [auth KK],
HA [auth B],
HB [auth D],
HC [auth G],
HD [auth I],
HE [auth L],
HF [auth GG],
HG [auth II],
HH [auth KK],
IA [auth B],
IB [auth D],
IC [auth G],
ID [auth I],
IE [auth L],
IF [auth GG],
IG [auth II],
IH [auth KK],
JA [auth B],
JB [auth D],
JC [auth G],
JD [auth I],
JE [auth L],
JF [auth GG],
JH [auth KK],
KA [auth B],
KB [auth D],
KC [auth G],
KD [auth J],
KE [auth L],
KF [auth GG],
KH [auth KK],
LA [auth B],
LB [auth E],
LC [auth G],
LE [auth M],
LF [auth GG],
LG [auth JJ],
LH [auth KK],
MA [auth B],
MB [auth E],
MC [auth G],
MD [auth J],
ME [auth M],
MF [auth GG],
MG [auth JJ],
NA [auth B],
NB [auth E],
NC [auth G],
ND [auth J],
NE [auth M],
NF [auth GG],
NG [auth JJ],
OA [auth B],
OB [auth E],
OC [auth G],
OD [auth J],
OE [auth M],
OF [auth HH],
OG [auth JJ],
PA [auth B],
PB [auth E],
PC [auth G],
PD [auth J],
PE [auth M],
PF [auth HH],
PG [auth JJ],
QA [auth B],
QB [auth E],
QC [auth G],
QD [auth J],
QE [auth N],
QF [auth HH],
QG [auth JJ],
RB [auth E],
RC [auth G],
RD [auth J],
RE [auth N],
RF [auth HH],
RG [auth JJ],
SB [auth E],
SC [auth G],
SD [auth K],
SE [auth N],
SF [auth HH],
SG [auth JJ],
TA [auth C],
TB [auth E],
TC [auth H],
TD [auth K],
TE [auth N],
TF [auth HH],
TG [auth JJ],
UA [auth C],
UB [auth E],
UD [auth K],
UF [auth HH],
V [auth A],
VA [auth C],
VD [auth K],
VE [auth O],
VF [auth HH],
VG [auth KK],
W [auth A],
WA [auth D],
WC [auth H],
WD [auth K],
WE [auth O],
WF [auth HH],
WG [auth KK],
X [auth A],
XA [auth D],
XC [auth H],
XD [auth K],
XE [auth O],
XF [auth HH],
XG [auth KK],
Y [auth A],
YA [auth D],
YB [auth F],
YC [auth H],
YD [auth K],
YE [auth O],
YF [auth HH],
YG [auth KK],
Z [auth A],
ZA [auth D],
ZB [auth F],
ZC [auth H],
ZD [auth K],
ZE [auth O],
ZG [auth KK]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
AF [auth GG]
GC [auth G]
JG [auth JJ]
LD [auth J]
U [auth A]
AF [auth GG],
GC [auth G],
JG [auth JJ],
LD [auth J],
U [auth A],
UC [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
RA [auth C],
SA [auth C],
VB [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth B]
FC [auth G]
KG [auth JJ]
UE [auth O]
UG [auth KK]
EA [auth B],
FC [auth G],
KG [auth JJ],
UE [auth O],
UG [auth KK],
VC [auth H],
WB [auth F],
XB [auth F],
ZF [auth II]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 234.65α = 90
b = 234.65β = 90
c = 234.65γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
d*TREKdata 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
  • Version 1.2: 2023-08-16
    Changes: Data collection
  • Version 1.3: 2023-10-18
    Changes: Refinement description