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- PDB-1c8n: TOBACCO NECROSIS VIRUS -

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Basic information

Entry
Database: PDB / ID: 1c8n
TitleTOBACCO NECROSIS VIRUS
ComponentsCOAT PROTEIN
KeywordsVIRUS / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesunidentified tobacco necrosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsOda, Y. / Fukuyama, K.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of tobacco necrosis virus at 2.25 A resolution.
Authors: Oda, Y. / Saeki, K. / Takahashi, Y. / Maeda, T. / Naitow, H. / Tsukihara, T. / Fukuyama, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystal Structural Analysis of Tobacco Necrosis Virus at 5 Angstrom Resolution
Authors: Bando, M. / Morimoto, Y. / Sato, T. / Tsukihara, T. / Yokota, Y. / Fukuyama, K. / Matsubara, H.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Symmetry and Subunit Arrangement of Tobacco Necrosis Virus (TNV)
Authors: Tsukihara, T. / Yokota, Y. / Koyama, T. / Fukuyama, K. / Matsubara, H.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Tobacco Necrosis Virus
Authors: Fukuyama, K. / Hirota, S. / Tsukihara, T.
History
DepositionMay 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: COAT PROTEIN
C: COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1568
Polymers89,9563
Non-polymers2005
Water3,459192
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,409,357480
Polymers5,397,334180
Non-polymers12,023300
Water3,243180
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: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 451 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)450,78040
Polymers449,77815
Non-polymers1,00225
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 541 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)540,93648
Polymers539,73318
Non-polymers1,20230
Water32418
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: COAT PROTEIN
C: COAT PROTEIN
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 451 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)450,78040
Polymers449,77815
Non-polymers1,00225
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)336.400, 336.400, 336.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)

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Components

#1: Protein COAT PROTEIN


Mass: 29985.188 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: THIS STRAIN IS CLOSE TO STRAIN A. / Source: (natural) unidentified tobacco necrosis virus / Genus: Necrovirus / Strain: TOYAMA ISOLATE / References: UniProt: Q9IPS9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2

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Sample preparation

Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
Conc.: 0.4 M / Common name: sodium phosphate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 298768 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 3.9
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.2 / % possible all: 95.6
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 842131
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
DMmodel building
X-PLOR3refinement
DENZOdata reduction
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TNV

1tnv


Resolution: 2.25→8 Å / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.273 -0.7 %
Rwork0.253 --
obs0.253 290000 99 %
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 5 192 4730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.64
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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