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- PDB-1a6c: STRUCTURE OF TOBACCO RINGSPOT VIRUS -

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Entry
Database: PDB / ID: 1a6c
TitleSTRUCTURE OF TOBACCO RINGSPOT VIRUS
ComponentsTOBACCO RINGSPOT VIRUS CAPSID PROTEIN
KeywordsVIRUS / TRSV / NEPOVIRUS / VIRUS STRUCTURE / VIRUS EVOLUTION / PICORNAVIRUS SUPERFAMILY / VIRUS CAPSID PROTEIN / Icosahedral virus
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Nepovirus coat protein / Nepovirus coat protein, C-terminal / Nepovirus coat protein, N-terminal / Nepovirus coat protein, central domain / Nepovirus coat protein, C-terminal domain / Nepovirus coat protein, N-terminal domain / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTobacco ringspot virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsJohnson, J.E. / Chandrasekar, V.
Citation
Journal: Structure / Year: 1998
Title: The structure of tobacco ringspot virus: a link in the evolution of icosahedral capsids in the picornavirus superfamily.
Authors: Chandrasekar, V. / Johnson, J.E.
#1: Journal: Virology / Year: 1995
Title: Expression of Tobacco Ringspot Virus Capsid Protein and Satellite RNA in Insect Cells and Three-Dimensional Structure of Tobacco Ringspot Virus-Like Particles
Authors: Singh, S. / Rothnagel, R. / Prasad, B.V. / Buckley, B.
#2: Journal: Virus Res. / Year: 1995
Title: Erratum. Nucleotide Sequence and in Vitro Expression of the Capsid Protein Gene of Tobacco Ringspot Virus
Authors: Buckley, B. / Silva, S. / Singh, S.
#3: Journal: Virus Res. / Year: 1993
Title: Nucleotide Sequence and in Vitro Expression of the Capsid Protein Gene of Tobacco Ringspot Virus
Authors: Buckley, B. / Silva, S. / Singh, S.
#4: Journal: Science / Year: 1989
Title: Protein-RNA Interactions in an Icosahedral Virus at 3.0 A Resolution
Authors: Chen, Z.G. / Stauffacher, C. / Li, Y. / Schmidt, T. / Bomu, W. / Kamer, G. / Shanks, M. / Lomonossoff, G. / Johnson, J.E.
#5: Journal: Nature / Year: 1985
Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses
Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G.
History
DepositionFeb 23, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / cell ...atom_site / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_z ..._atom_site.Cartn_x / _atom_site.Cartn_z / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][3] / _pdbx_database_status.process_site / _pdbx_struct_oper_list.id / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[2] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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: TOBACCO RINGSPOT VIRUS CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)56,9941
Polymers56,9941
Non-polymers00
Water00
1
A: TOBACCO RINGSPOT VIRUS CAPSID PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)3,419,61960
Polymers3,419,61960
Non-polymers00
Water0
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: TOBACCO RINGSPOT VIRUS CAPSID PROTEIN
x 5


  • icosahedral pentamer
  • 285 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)284,9685
Polymers284,9685
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: TOBACCO RINGSPOT VIRUS CAPSID PROTEIN
x 6


  • icosahedral 23 hexamer
  • 342 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)341,9626
Polymers341,9626
Non-polymers00
Water0
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: TOBACCO RINGSPOT VIRUS CAPSID PROTEIN
x 30


  • crystal asymmetric unit, crystal frame
  • 1.71 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)1,709,80930
Polymers1,709,80930
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)407.060, 399.680, 285.970
Angle α, β, γ (deg.)90.00, 129.10, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.33355445, -0.85735106, 0.39198756), (0.72047793, 0.5, 0.48057056), (-0.60801255, 0.12211636, 0.78447952)
3generate(-0.7447773, -0.6667807, 0.02623772), (0.30836465, -0.30901699, 0.89970144), (-0.59179655, 0.67813618, 0.43576031)
4generate(-0.74477743, 0.30834932, -0.59179565), (-0.66681329, -0.30901699, 0.678168), (0.02623803, 0.89965896, 0.43576045)
5generate(0.33355423, 0.72044246, -0.60801146), (-0.85739312, 0.5, 0.12212193), (0.39198842, 0.48054775, 0.78447975)
6generate(-0.11076353, -0.41209313, -0.90437867), (-0.41211327, -0.80901699, 0.41913088), (-0.90438043, 0.41911121, -0.08021948)
7generate(0.21602391, -0.22152278, -0.95092432), (-0.97517795, -0.22153344), (0.0490747, 0.97513102, -0.21602391)
8generate(0.49062739, -0.41209313, -0.7677593), (-0.19057983, 0.80901699, -0.55604607), (0.85027471, 0.41911121, 0.31838961)
9generate(0.33355423, -0.72044246, -0.60801146), (0.85739312, 0.5, -0.12212193), (0.39198842, -0.48054775, 0.78447975)
10generate(-0.03812578, -0.72044246, -0.69244688), (0.72047793, -0.5, 0.48057056), (-0.6924481, -0.48054775, 0.53812578)
11generate(-0.92736226, -0.30834932, 0.21193179), (-0.30836465, 0.30901699, -0.89970144), (0.21193233, -0.89965896, -0.38165473)
12generate(-0.66034189, 0.6667807, -0.34544191), (0.66681329, 0.30901699, -0.678168), (-0.34544258, -0.67813618, -0.6486751)
13generate(0.47017382, 0.85735106, -0.20940274), (0.85739312, -0.5, -0.12212193), (-0.20940346, -0.12211636, -0.97017382)
14generate(0.90185059, 0.43204782), (-1), (0.43204826, -0.90185059)
15generate(0.03812578, -0.72044246, 0.69244688), (-0.72047793, -0.5, -0.48057056), (0.6924481, -0.48054775, -0.53812578)
16generate(0.21602413, 0.97513002, 0.0490747), (0.22153344, -0.97517695), (-0.95092627, 0.22152278, -0.21602413)
17generate(0.74477743, 0.30834932, 0.59179565), (0.66681329, -0.30901699, -0.678168), (-0.02623803, 0.89965896, -0.43576045)
18generate(0.11076353, -0.41209313, 0.90437867), (0.41211327, -0.80901699, -0.41913088), (0.90438043, 0.41911121, 0.08021948)
19generate(-0.80983193, -0.19057036, 0.55484465), (-0.19057983, -0.80901699, -0.55604607), (0.55484605, -0.55601981, 0.61884892)
20generate(-0.7447773, 0.6667807, 0.02623772), (-0.30836465, -0.30901699, -0.89970144), (-0.59179655, -0.67813618, 0.43576031)
21generate(-0.49062774, 0.19057036, -0.8502731), (-0.41211327, 0.80901699, 0.41913088), (0.76776084, 0.55601981, -0.31838924)
22generate(0.49062739, 0.41209313, -0.7677593), (0.19057983, 0.80901699, 0.55604607), (0.85027471, -0.41911121, 0.31838961)
23generate(0.92736226, -0.30834932, -0.21193179), (0.30836465, 0.30901699, 0.89970144), (-0.21193233, -0.89965896, 0.38165473)
24generate(0.21602413, -0.97513002, 0.0490747), (-0.22153344, 0.97517695), (-0.95092627, -0.22152278, -0.21602413)
25generate(-0.66034189, -0.6667807, -0.34544191), (-0.66681329, 0.30901699, 0.678168), (-0.34544258, 0.67813618, -0.6486751)
26generate(-0.47017382, 0.85735106, 0.20940274), (-0.85739312, -0.5, 0.12212193), (0.20940346, -0.12211636, 0.97017382)
27generate(0.33355445, 0.85735106, 0.39198756), (-0.72047793, 0.5, -0.48057056), (-0.60801255, -0.12211636, 0.78447952)
28generate(0.49062774, 0.19057036, 0.8502731), (0.41211327, 0.80901699, -0.41913088), (-0.76776084, 0.55601981, 0.31838924)
29generate(-0.21602391, -0.22152278, 0.95092432), (0.97517795, 0.22153344), (-0.0490747, 0.97513102, 0.21602391)
30generate(-0.80983193, 0.19057036, 0.55484465), (0.19057983, -0.80901699, 0.55604607), (0.55484605, 0.55601981, 0.61884892)

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Components

#1: Protein TOBACCO RINGSPOT VIRUS CAPSID PROTEIN / TRSV


Mass: 56993.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tobacco ringspot virus / Genus: Nepovirus / Strain: XANTHI-NC / References: UniProt: Q88894

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 27

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 2-3 % / Common name: PEG MW 3350

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 1, 1994 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 92395 / % possible obs: 18 % / Observed criterion σ(I): 4 / Redundancy: 1.2 % / Rmerge(I) obs: 0.084 / Rsym value: 0.15
Reflection shellResolution: 3.5→4 Å / % possible all: 10

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Processing

Software
NameVersionClassification
RAVEmodel building
X-PLOR3.1refinement
PURDUE(OSC)data reduction
PROGRAMSDEVELOPED BY M. G. ROSSMANN AT PURDUE UNIVERSITYdata scaling
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF COMOVIRUS CPMV

Resolution: 3.5→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 1
Details: THE STRUCTURE WAS REFINED TO 3.5 ANGSTROMS RESOLUTION USING ONLY 27% OF THE THEORETICALLY POSSIBLE UNIQUE REFLECTIONS BETWEEN 8.0 AND 3.5 ANGSTROMS. THERE ARE STILL SOME BOND ANGLES AND BOND ...Details: THE STRUCTURE WAS REFINED TO 3.5 ANGSTROMS RESOLUTION USING ONLY 27% OF THE THEORETICALLY POSSIBLE UNIQUE REFLECTIONS BETWEEN 8.0 AND 3.5 ANGSTROMS. THERE ARE STILL SOME BOND ANGLES AND BOND LENGTHS IN THE CRYSTAL STRUCTURE WHICH VARY BY GREATER THAN 3.0 RMSD FROM THEIR CORRESPONDING E & H VALUES. THESE HAVE NOT BEEN FIXED AT PRESENT.
RfactorNum. reflection% reflection
Rwork0.269 --
obs0.269 71615 27.5 %
Displacement parametersBiso mean: 15 Å2
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4888 0 0 0 4888
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3.5→3.64 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rwork0.324 3955
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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