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- PDB-7m3t: Crystallographic structure of a cubic crystal of STMV (80.7 degre... -

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Basic information

Entry
Database: PDB / ID: 7m3t
TitleCrystallographic structure of a cubic crystal of STMV (80.7 degree rotation about 111) grown from chloride
Components
  • (Coat protein) x 3
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS/RNA / VIRUS-RNA complex
Function / homologySatellite virus coat domain superfamily / viral capsid / structural molecule activity / PHOSPHATE ION / RNA / RNA (> 10) / Coat protein
Function and homology information
Biological speciesSatellite tobacco mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.
Authors: McPherson, A.
History
DepositionMar 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,56367
Polymers412,22039
Non-polymers1,34228
Water19,0601058
1
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules

A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules

A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
a: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
e: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
h: RNA (5'-R(P*UP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
n: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
GG: Coat protein
HH: Coat protein
II: Coat protein
JJ: Coat protein
KK: Coat protein
TT: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
UU: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
bb: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,240,582198
Polymers1,236,661117
Non-polymers3,92181
Water2,108117
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
Unit cell
Length a, b, c (Å)234.050, 234.050, 234.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Space group name HallP223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
Components on special symmetry positions
IDModelComponents
11D-201-

CL

21M-201-

CL

31JJ-203-

CL

41KK-201-

CL

51bb-202-

CL

61bb-203-

CL

71U-5-

CL

81D-339-

HOH

91M-330-

HOH

101KK-345-

HOH

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Components

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Protein , 3 types, 20 molecules ABCDEFHIJKLMOGGHHIIJJKKGN

#1: Protein
Coat protein


Mass: 17533.949 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574
#2: Protein Coat protein


Mass: 17519.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574
#3: Protein Coat protein


Mass: 17562.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574

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RNA chain , 7 types, 19 molecules PSTVXYaTTUUeWWhillmkknqqbb

#4: RNA chain
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3247.100 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide decamer / Source: (natural) Satellite tobacco mosaic virus
#5: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3629.032 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide dodecamer / Source: (natural) Satellite tobacco mosaic virus
#6: RNA chain RNA (5'-R(P*UP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3652.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA nucleotide dodecamer / Source: (natural) Satellite tobacco mosaic virus
#7: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3322.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide undecamer / Source: (natural) Satellite tobacco mosaic virus
#8: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3016.700 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide decamer / Source: (natural) Satellite tobacco mosaic virus
#9: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2404.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide octamer / Source: (natural) Satellite tobacco mosaic virus
#10: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3905.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide dodecamer / Source: (natural) Satellite tobacco mosaic virus

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Non-polymers , 4 types, 1086 molecules

#11: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#12: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1058 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.54 % / Description: Crystals were large octahedra
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were equal volumes of 5 mg/ml STMV in 0.1 M phosphate at pH 6.5 and the reservoir ...Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were equal volumes of 5 mg/ml STMV in 0.1 M phosphate at pH 6.5 and the reservoir solution, which was 8% w/v NaCl in 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.
PH range: 4.5 - 7.0

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→75 Å / Num. obs: 69957 / % possible obs: 99 % / Redundancy: 9.55 % / Biso Wilson estimate: 34.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.23 / Rsym value: 0.21 / Net I/σ(I): 9.9
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1238 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQ8

4oq8


Resolution: 3.2→46.81 Å / Cross valid method: FREE R-VALUE / Phase error: 27.6253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2536 3540 5.06 %
Rwork0.215 66415 -
obs0.2184 69955 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.13 Å2
Refinement stepCycle: LAST / Resolution: 3.2→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22493 2806 56 1058 26413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003226169
X-RAY DIFFRACTIONf_angle_d0.55336241
X-RAY DIFFRACTIONf_chiral_restr0.04434329
X-RAY DIFFRACTIONf_plane_restr0.00544224
X-RAY DIFFRACTIONf_dihedral_angle_d13.04769901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.260.24931550.21433056X-RAY DIFFRACTION87.34
3.26-3.310.24041810.21183181X-RAY DIFFRACTION91.28
3.31-3.380.29631760.20393334X-RAY DIFFRACTION94.31
3.38-3.450.26332050.19913276X-RAY DIFFRACTION93.87
3.45-3.520.24122000.19643262X-RAY DIFFRACTION94.17
3.52-3.60.26051840.20053297X-RAY DIFFRACTION94.71
3.6-3.690.25311860.19313270X-RAY DIFFRACTION94.59
3.69-3.790.23321420.19243413X-RAY DIFFRACTION95.98
3.79-3.910.23121550.193324X-RAY DIFFRACTION95.52
3.91-4.030.22951950.19323300X-RAY DIFFRACTION94.42
4.03-4.180.22231810.19813328X-RAY DIFFRACTION94.84
4.18-4.340.23571610.21033357X-RAY DIFFRACTION95.42
4.34-4.540.25461750.20553327X-RAY DIFFRACTION95
4.54-4.780.24161470.20453360X-RAY DIFFRACTION95.78
4.78-5.080.21561740.20093360X-RAY DIFFRACTION95.08
5.08-5.470.24881970.21323318X-RAY DIFFRACTION94.4
5.47-6.020.22652040.21783362X-RAY DIFFRACTION94.28
6.02-6.890.26291900.23873353X-RAY DIFFRACTION94.64
6.89-8.670.24691820.25153406X-RAY DIFFRACTION94.93
8.67-46.810.36081410.3183540X-RAY DIFFRACTION95.78
Refinement TLS params.Method: refined / Origin x: 87.281597292 Å / Origin y: 173.324634474 Å / Origin z: 26.6288012689 Å
111213212223313233
T-0.0504035373839 Å20.0851078763492 Å2-0.0161594663142 Å2-0.0244061432217 Å20.0229234332838 Å2--0.0499671716393 Å2
L-0.0605900991688 °2-0.0297113614253 °20.0663521071633 °2--0.0918101377866 °2-0.00899047802159 °2---0.0724277771473 °2
S-0.00491580166004 Å °-0.0680354708074 Å °-0.0901293847373 Å °0.0487037930943 Å °0.02174063879 Å °-0.147786175662 Å °0.143035735103 Å °0.11611912705 Å °-0.000575082048273 Å °
Refinement TLS groupSelection details: all

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