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- PDB-2tbv: STRUCTURE OF TOMATO BUSHY STUNT VIRUS. V. COAT PROTEIN SEQUENCE D... -

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Entry
Database: PDB / ID: 2tbv
TitleSTRUCTURE OF TOMATO BUSHY STUNT VIRUS. V. COAT PROTEIN SEQUENCE DETERMINATION AND ITS STRUCTURAL IMPLICATIONS
ComponentsTOMATO BUSHY STUNT VIRUS
KeywordsVIRUS / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / RNA binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / 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 speciesTomato bushy stunt virus
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsHarrison, S.C.
Citation
Journal: J.Mol.Biol. / Year: 1984
Title: Structure of tomato bushy stunt virus. V. Coat protein sequence determination and its structural implications
Authors: Hopper, P. / Harrison, S.C. / Sauer, R.T.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of Tomato Bushy Stunt Virus. Iv. The Virus Particle at 2.9 Angstroms Resolution
Authors: Olson, A.J. / Bricogne, G. / Harrison, S.C.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Divalent Cation Sites in Tomato Bushy Stunt Virus. Difference Maps at 2.9 Angstroms Resolution
Authors: Hogle, J. / Kirchhausen, T. / Harrison, S.C.
#3: Journal: Biophys.J. / Year: 1980
Title: Protein Interfaces and Intersubunit Bonding. The Case of Tomato Bushy Stunt Virus
Authors: Harrison, S.C.
#4: Journal: Nature / Year: 1978
Title: Tomato Bushy Stunt Virus at 2.9 Angstroms Resolution
Authors: Harrison, S.C. / Olson, A.J. / Schutt, C.E. / Winkler, F.K. / Bricogne, G.
#5: Journal: Nature / Year: 1977
Title: Tomato Bushy Stunt Virus at 5.5-Angstroms Resolution
Authors: Winkler, F.K. / Schutt, C.E. / Harrison, S.C. / Bricogne, G.
#6: Journal: J.Mol.Biol. / Year: 1969
Title: Structure of Tomato Bushy Stunt Virus. I. The Spherically Averaged Electron Density
Authors: Harrison, S.C.
History
DepositionJun 22, 1984Processing site: BNL
Revision 1.0Jul 20, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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

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Assembly

Deposited unit
A: TOMATO BUSHY STUNT VIRUS
B: TOMATO BUSHY STUNT VIRUS
C: TOMATO BUSHY STUNT VIRUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,9699
Polymers121,7283
Non-polymers2406
Water0
1
A: TOMATO BUSHY STUNT VIRUS
B: TOMATO BUSHY STUNT VIRUS
C: TOMATO BUSHY STUNT VIRUS
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,318,110540
Polymers7,303,682180
Non-polymers14,428360
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: TOMATO BUSHY STUNT VIRUS
B: TOMATO BUSHY STUNT VIRUS
C: TOMATO BUSHY STUNT VIRUS
hetero molecules
x 5


  • icosahedral pentamer
  • 610 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)609,84345
Polymers608,64015
Non-polymers1,20230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: TOMATO BUSHY STUNT VIRUS
B: TOMATO BUSHY STUNT VIRUS
C: TOMATO BUSHY STUNT VIRUS
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 732 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)731,81154
Polymers730,36818
Non-polymers1,44336
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
A: TOMATO BUSHY STUNT VIRUS
B: TOMATO BUSHY STUNT VIRUS
C: TOMATO BUSHY STUNT VIRUS
hetero molecules
x 5


  • crystal asymmetric unit, crystal frame
  • 610 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)609,84345
Polymers608,64015
Non-polymers1,20230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)383.200, 383.200, 383.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Atom site foot note1: THE CHEMICAL SEQUENCE IN RESIDUES 246 TO 258, 269 TO 275 AND 365 TO 379 COULD NOT BE DETERMINED WELL. RESIDUES AT THESE POSITIONS IN THE COORDINATE LIST WERE BUILT TO FIT THE OBSERVED ELECTRON ...1: THE CHEMICAL SEQUENCE IN RESIDUES 246 TO 258, 269 TO 275 AND 365 TO 379 COULD NOT BE DETERMINED WELL. RESIDUES AT THESE POSITIONS IN THE COORDINATE LIST WERE BUILT TO FIT THE OBSERVED ELECTRON DENSITY. THESE COORDINATES SHOULD BE REGARDED ONLY AS AN APPROXIMATION TO THE CORRECT MODEL IN THIS REGION (SEE REFERENCE 1 ABOVE).
2: RESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS RESIDUE WAS BUILT AS GLY IN THIS MODEL. SIMILARLY, RESIDUE 107 IS GLY IN THE CHEMICAL SEQUENCE, BUT ...2: RESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS RESIDUE WAS BUILT AS GLY IN THIS MODEL. SIMILARLY, RESIDUE 107 IS GLY IN THE CHEMICAL SEQUENCE, BUT APPEARS TO HAVE A SIDE CHAIN IN THE ELECTRON DENSITY. THIS RESIDUE WAS BUILT AS SER. THE DISCREPANCY BETWEEN THE CHEMICAL AND THE CRYSTALLOGRAPHIC DATA IS PRESENTLY UNRESOLVED.
3: THE S (SHELL) AND P (PROJECTION) DOMAINS OF EACH SUBUNIT WERE BUILT SEPARATELY. TO FACILITATE THE MERGING OF THE DOMAINS INTO A SINGLE CONTIGUOUS CHAIN, AN OVERLAP REGION WAS BUILT. THE ATOMS IN ...3: THE S (SHELL) AND P (PROJECTION) DOMAINS OF EACH SUBUNIT WERE BUILT SEPARATELY. TO FACILITATE THE MERGING OF THE DOMAINS INTO A SINGLE CONTIGUOUS CHAIN, AN OVERLAP REGION WAS BUILT. THE ATOMS IN THIS OVERLAP REGION ARE PRESENTED IN THIS ENTRY AS ALTERNATE LOCATIONS *S* AND *P* IN RESIDUES 273, 274 AND 275.
4: CAREFUL MODEL BUILDING AGAINST THE ELECTRON DENSITY INDICATES THAT PRO 290 AND PRO 359 ARE CIS-PROLINES. HOWEVER, THE USUAL CAVEATS APPLIED TO A 2.9 ANGSTROMS STUDY SHOULD BE OBSERVED.
5: SEE REMARK 3. / 6: SEE REMARK 3 AND FTNOTE 1.
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 TOMATO BUSHY STUNT VIRUS /


Mass: 40576.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tomato bushy stunt virus / Genus: Tombusvirus / References: UniProt: P11795
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
Compound detailsTHE S (SHELL) AND P (PROJECTION) DOMAINS OF EACH SUBUNIT WERE BUILT SEPARATELY. TO FACILITATE THE ...THE S (SHELL) AND P (PROJECTION) DOMAINS OF EACH SUBUNIT WERE BUILT SEPARATELY. TO FACILITATE THE MERGING OF THE DOMAINS INTO A SINGLE CONTIGUOUS CHAIN, AN OVERLAP REGION WAS BUILT. THE ATOMS IN THIS OVERLAP REGION ARE PRESENTED IN THIS ENTRY AS ALTERNATE LOCATIONS *S* AND *P* IN RESIDUES 273, 274 AND 275.
Sequence detailsRESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS ...RESIDUE 102 IS SER IN THE CHEMICAL SEQUENCE, BUT SHOWS NO SIDE CHAIN DENSITY IN THE MAP. THIS RESIDUE WAS BUILT AS GLY IN THIS MODEL. SIMILARLY, RESIDUE 107 IS GLY IN THE CHEMICAL SEQUENCE, BUT APPEARS TO HAVE A SIDE CHAIN IN THE ELECTRON DENSITY. THIS RESIDUE WAS BUILT AS SER. THE DISCREPANCY BETWEEN THE CHEMICAL AND THE CRYSTALLOGRAPHIC DATA IS PRESENTLY UNRESOLVED. THE CHEMICAL SEQUENCE IN RESIDUES 246 TO 258, 269 TO 275 AND 365 TO 379 COULD NOT BE DETERMINED WELL. RESIDUES AT THESE POSITIONS IN THE COORDINATE LIST WERE BUILT TO FIT THE OBSERVED ELECTRON DENSITY. THESE COORDINATES SHOULD BE REGARDED ONLY AS AN APPROXIMATION TO THE CORRECT MODEL IN THIS REGION (SEE REFERENCE 1 ABOVE)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: other
Details: Harrison, S.C., (1980) Biophys, J., 32, 139., Harrison, S.C., (1978) Nature, 276, 386., Olson, A.J., (1983) J. Mol. Biol., 171, 61.

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Processing

RefinementHighest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 6 0 6648

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