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- PDB-7m50: Crystallographic structure of a cubic crystal form of STMV grown ... -

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Basic information

Entry
Database: PDB / ID: 7m50
TitleCrystallographic structure of a cubic crystal form of STMV grown from ammonium sulfate
Components
  • (RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)- ...) x 2
  • Coat protein
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*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*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U))-3')
KeywordsVIRUS / RNA / ions / ion channel / decapsidation
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: 2.31 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 22, 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

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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*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Y: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
a: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-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*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*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*A)-3')
UU: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U))-3')
bb: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,48957
Polymers402,18539
Non-polymers1,30318
Water77,7894318
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*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Y: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
a: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-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*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*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*A)-3')
UU: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U))-3')
bb: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*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*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Y: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
a: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-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*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*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*A)-3')
UU: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U))-3')
bb: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*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*A)-3')
S: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
T: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
V: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3')
X: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
Y: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
a: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-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*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
i: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
m: RNA (5'-R(P*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*A)-3')
UU: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
WW: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U))-3')
bb: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
kk: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3')
ll: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
qq: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,210,181168
Polymers1,206,556117
Non-polymers3,62551
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
11F-201-

SO4

21M-201-

SO4

31M-202-

SO4

41O-201-

SO4

51II-201-

PO4

61KK-201-

SO4

71R-1-

PO4

81D-325-

HOH

91D-348-

HOH

101D-357-

HOH

111D-373-

HOH

121D-375-

HOH

131E-235-

HOH

141E-306-

HOH

151E-309-

HOH

161F-331-

HOH

171H-646-

HOH

181I-238-

HOH

191J-354-

HOH

201M-310-

HOH

211e-391-

HOH

221e-392-

HOH

231II-404-

HOH

241II-560-

HOH

251JJ-394-

HOH

261KK-341-

HOH

271KK-487-

HOH

281KK-491-

HOH

291bb-282-

HOH

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Components

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Protein , 1 types, 20 molecules ABCDEFGHIJKLMNOGGHHIIJJKK

#1: Protein
Coat protein


Mass: 17533.949 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Satellite tobacco mosaic virus / References: UniProt: P17574

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RNA chain , 6 types, 15 molecules PVTTSTYaeWWillqqmnkk

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


Mass: 2588.689 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide octamer / Source: (natural) Satellite tobacco mosaic virus
#3: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide hexamer / Source: (natural) Satellite tobacco mosaic virus
#5: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2259.483 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide heptamer / Source: (natural) Satellite tobacco mosaic virus
#6: 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
#8: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2710.535 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide nonamer / 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.: 3 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide octamer / Source: (natural) Satellite tobacco mosaic virus

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RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)- ... , 2 types, 4 molecules XUUbbh

#4: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


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


Mass: 3016.700 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide decamer / Source: (natural) Satellite tobacco mosaic virus

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Non-polymers , 5 types, 4336 molecules

#10: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#11: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Mg
#12: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#13: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4318 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.7 % / Description: 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. Drops were 6 to 8 ul and were composed of equal volumes of a 5 mg/ml virus stock solution ...Details: Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. Drops were 6 to 8 ul and were composed of equal volumes of a 5 mg/ml virus stock solution containing 0.1 M phosphate at pH 6.5, and the reservoir solution. The reservoir solution was 18% ammonium sulfate 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: Jun 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→80 Å / Num. obs: 159229 / % possible obs: 0.99 % / Redundancy: 10.17 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.91 / Rmerge(I) obs: 0.18 / Rsym value: 0.18 / Net I/σ(I): 12.8
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 854 / CC1/2: 0.41 / % possible all: 0.25

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Processing

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

4oq8


Resolution: 2.31→74.01 Å / Cross valid method: FREE R-VALUE / σ(F): 493.22 / Phase error: 29.3629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2708 2152 1.35 %
Rwork0.2459 157026 -
obs0.2484 159178 85.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.25 Å2
Refinement stepCycle: LAST / Resolution: 2.31→74.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22607 2796 66 4318 29787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001626264
X-RAY DIFFRACTIONf_angle_d0.489636378
X-RAY DIFFRACTIONf_chiral_restr0.05224348
X-RAY DIFFRACTIONf_plane_restr0.00424243
X-RAY DIFFRACTIONf_dihedral_angle_d11.35819932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.370.4426400.36832974X-RAY DIFFRACTION22.66
2.37-2.430.36821010.33897682X-RAY DIFFRACTION58.24
2.43-2.510.31481260.30689691X-RAY DIFFRACTION73.92
2.51-2.590.32621370.293310656X-RAY DIFFRACTION81.44
2.59-2.680.31511410.271511292X-RAY DIFFRACTION85.6
2.68-2.790.24731530.256911838X-RAY DIFFRACTION89.62
2.79-2.910.26871560.234512386X-RAY DIFFRACTION94.23
2.91-3.070.24531620.232512766X-RAY DIFFRACTION96.74
3.07-3.260.23721630.223312843X-RAY DIFFRACTION97.19
3.26-3.510.23621600.211112847X-RAY DIFFRACTION97.41
3.51-3.860.21811620.210412906X-RAY DIFFRACTION97.43
3.86-4.420.20961620.218112995X-RAY DIFFRACTION97.7
4.42-5.570.23751610.224413043X-RAY DIFFRACTION97.67
5.57-74.010.3221640.28113271X-RAY DIFFRACTION97.27
Refinement TLS params.Method: refined / Origin x: 86.8718149837 Å / Origin y: 172.931438482 Å / Origin z: 26.4749047371 Å
111213212223313233
T0.0707857517812 Å20.0239932782917 Å2-0.0111527613392 Å2-0.074806382452 Å2-0.00322871230631 Å2--0.0815839884117 Å2
L-0.0032504217873 °2-0.00776378456689 °20.00394889604966 °2--0.00485298388746 °20.0110171562196 °2---0.00543501693158 °2
S-0.0089663285677 Å °-0.0253631303234 Å °-0.0270431075343 Å °0.0166107029725 Å °0.00423831167318 Å °-0.0180164197673 Å °0.0384082652823 Å °0.010431206784 Å °-0.00270874938477 Å °
Refinement TLS groupSelection details: all

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