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- PDB-4oq8: Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using ... -

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Basic information

Entry
Database: PDB / ID: 4oq8
TitleSatellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints
Components
  • Coat protein
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • RNA (5'-R(P*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS/RNA / Double-helix RNA / Protein-RNA complex / Swiss Jelly-roll beta barrel / VIRUS-RNA complex
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Satellite virus coat domain / Satellite virus coat domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / RNA / Coat protein
Similarity search - Component
Biological speciesSatellite Tobacco Mosaic Virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLarson, S.B. / Day, J.S. / McPherson, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Satellite tobacco mosaic virus refined to 1.4 angstrom resolution.
Authors: Larson, S.B. / Day, J.S. / McPherson, A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Refined structure of satellite tobacco mosaic virus at 1.8 A resolution.
Authors: Larson, S.B. / Day, J. / Greenwood, A. / McPherson, A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Three-dimensional structure of satellite tobacco mosaic virus at 2.9 A resolution.
Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A.
#3: Journal: Nature / Year: 1993
Title: Double-helical RNA in satellite tobacco mosaic virus.
Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A.
#4: Journal: Protein Sci. / Year: 1992
Title: Macromolecular crystal growth experiments on International Microgravity Laboratory--1.
Authors: Day, J. / McPherson, A.
#5: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary analysis of crystals of satellite tobacco mosaic virus.
Authors: Koszelak, S. / Dodds, J.A. / McPherson, A.
#6: Journal: Curr.Opin.Struct.Biol. / Year: 2001
Title: Satellite tobacco mosaic virus RNA: structure and implications for assembly.
Authors: Larson, S.B. / McPherson, A.
#7: Journal: J.Struct.Biol. / Year: 2012
Title: A model for the structure of satellite tobacco mosaic virus.
Authors: Zeng, Y. / Larson, S.B. / Heitsch, C.E. / McPherson, A. / Harvey, S.C.
History
DepositionFeb 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coat protein
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6778
Polymers24,3654
Non-polymers3114
Water4,990277
1
A: Coat protein
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*U)-3')
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,480,592480
Polymers1,461,907240
Non-polymers18,684240
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Coat protein
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*U)-3')
hetero molecules
x 5


  • icosahedral pentamer
  • 123 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)123,38340
Polymers121,82620
Non-polymers1,55720
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*U)-3')
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 148 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)148,05948
Polymers146,19124
Non-polymers1,86824
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Coat protein
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*U)-3')
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 370 kDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)370,148120
Polymers365,47760
Non-polymers4,67160
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)172.690, 190.300, 201.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, 0.309017, 0.80901699), (0.309017, 0.80901699, -0.5), (-0.80901699, 0.5, 0.309017)
3generate(-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.30901699), (-0.5, 0.309017, -0.80901699)
4generate(-0.30901699, 0.809017, -0.5), (0.80901699, 0.5, 0.309017), (0.5, -0.309017, -0.809017)
5generate(0.5, 0.30901699, -0.80901699), (0.30901699, 0.809017, 0.5), (0.809017, -0.5, 0.30901699)
6generate(-0.80901699, 0.50000001, 0.309017), (0.49999999, 0.30901699, 0.809017), (0.30901699, 0.80901699, -0.5)
7generate(-0.5, 0.309017, -0.80901699), (-0.309017, 0.80901699, 0.5), (0.80901699, 0.5, -0.309017)
8generate(0.5, -0.30901699, -0.809017), (-0.309017, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699)
9generate(0.809017, -0.5, 0.30901699), (0.5, 0.30901699, -0.809017), (0.30901699, 0.80901699, 0.5)
10generate(1), (1), (1)
11generate(0.80901699, 0.5, 0.30901699), (0.50000001, -0.309017, -0.80901699), (-0.30901699, 0.809017, -0.49999999)
12generate(0.309017, 0.80901699, 0.5), (0.80901699, -0.5, 0.309017), (0.5, 0.309017, -0.80901699)
13generate(1), (1), (1)
14generate(0.30901699, 0.80901699, -0.5), (-0.809017, 0.5, 0.30901699), (0.5, 0.309017, 0.80901699)
15generate(0.80901699, 0.5, -0.309017), (-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.809017, 0.5)

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Coat protein


Mass: 17533.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: grown in Nicotiana Tobacum plants / Source: (natural) Satellite Tobacco Mosaic Virus / References: UniProt: P17574

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RNA chain , 3 types, 3 molecules BCD

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


Mass: 3247.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide decamer / Source: (natural) Satellite Tobacco Mosaic Virus
#3: 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
#4: RNA chain RNA (5'-R(P*UP*U)-3')


Mass: 567.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide dimer / Source: (natural) Satellite Tobacco Mosaic Virus

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Non-polymers , 4 types, 281 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.06 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 3, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 1.4→48.35 Å / Num. all: 643001 / Num. obs: 613720 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 7.23 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.4-1.452.170.3542.98315274307067.3
1.45-1.512.90.3633.27053586111195.5
1.51-1.584.010.3873.75613276270098
1.58-1.665.740.4194.15106476350899
1.66-1.767.140.4134.74837166376199.5
1.76-1.97.610.45.24552936359699.1
1.9-2.098.060.35963648316331898.6
2.09-2.398.850.2667.72513726344198.6
2.39-3.0211.010.14614.21771486409199.2
3.02-48.3512.770.06631.4933746512499.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
Coot0.6.2model building
CNS1.2refinement
d*TREKdata reduction
d*TREKdata scaling
CNS1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A34

1a34


Resolution: 1.45→48.35 Å / Num. parameters: 13624 / Num. restraintsaints: 12660 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THOUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens were included in the refinements. Strict icosahedral symmetry was applied.
RfactorNum. reflection% reflectionSelection details
Rfree0.2793 28359 5 %RANDOM
Rwork0.2776 ---
all0.2784 570721 --
obs0.2784 570721 98.5 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: CNS 1.2 method / Bsol: 82.47 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 161.95 Å2 / Biso mean: 39.23 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å20 Å2
2--2.396 Å20 Å2
3----0.316 Å2
Refine analyzeNum. disordered residues: 88
FreeObs
Luzzati coordinate error0.3 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.45→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 448 16 277 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0068
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_dihedral_angle_d17.992
X-RAY DIFFRACTIONc_improper_angle_d1.401
X-RAY DIFFRACTIONc_mcbond_it1.182
X-RAY DIFFRACTIONc_mcangle_it1.818
X-RAY DIFFRACTIONc_scbond_it7.7920
X-RAY DIFFRACTIONc_scangle_it10.1232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.45-1.50.517127025.30.5216511940.00995389693.33
1.5-1.560.433427090.4295535710.00835628097.63
1.56-1.630.340827980.3442545010.00645729999.06
1.63-1.720.320829500.3136544610.00595741199.39
1.72-1.830.322128670.3244545940.0065746199.34
1.83-1.970.378127970.3682543940.00715719198.72
1.97-2.160.366629530.3601541410.00675709498.54
2.16-2.480.308928200.3087545780.00585739898.76
2.48-3.120.249628710.246549860.00475785799.28
3.12-48.350.212128920.214559420.00395883499.39
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN-ALLHDG.PARAMPROTEIN-ALLHDG.TOP
X-RAY DIFFRACTION2DNA-RNA-ALLATOM.PARAMDNA-RNA-ALLATOM.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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