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- PDB-4sbv: The REFINEMENT OF SOUTHERN BEAN MOSAIC VIRUS IN RECIPROCAL SPACE -

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Entry
Database: PDB / ID: 4sbv
TitleThe REFINEMENT OF SOUTHERN BEAN MOSAIC VIRUS IN RECIPROCAL SPACE
ComponentsSOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
KeywordsVIRUS / COAT PROTEIN (VIRAL) / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural constituent of virion / lipid binding / calcium ion binding / 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 speciesSouthern bean mosaic virus
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsRossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Refined structure of southern bean mosaic virus at 2.9 A resolution.
Authors: Silva, A.M. / Rossmann, M.G.
#1: Journal: J.Mol.Biol. / Year: 1983
Title: Subunit Interactions in Southern Bean Mosaic Virus
Authors: Rossmann, M.G. / Abad-Zapatero, C. / Hermodson, M.A. / Erickson, J.W.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Structural Comparisons of Small Spherical Plant Viruses
Authors: Rossmann, M.G. / Abad-Zapatero, C. / Murthy, M.R. / Liljas, L. / Jones, T.A. / Strandberg, B.
#3: Journal: Virology / Year: 1982
Title: Amino Acid Sequence of Southern Bean Mosaic Virus Coat Protein and its Relation to the Three-Dimensional Structure of the Virus
Authors: Hermodson, M.A. / Abad-Zapatero, C. / Abdel-Meguid, S.S. / Pundak, S. / Rossmann, M.G. / Tremaine, J.H.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1981
Title: A Description of Techniques Used in the Structure Determination of Southern Bean Mosaic Virus at 2.8 Angstroms Resolution
Authors: Abad-Zapatero, C. / Abdel-Meguid, S.S. / Johnson, J.E. / Leslie, A.G.W. / Rayment, I. / Rossmann, M.G. / Suck, D. / Tsukihara, T.
#5: Journal: Nature / Year: 1980
Title: Southern Bean Mosaic Virus at 2.8 Angstroms Resolution
Authors: Abad-Zapatero, C. / Abdel-Meguid, S.S. / Johnson, J.E. / Leslie, A.G.W. / Rayment, I. / Rossmann, M.G. / Suck, D. / Tsukihara, T.
#6: Journal: J.Biol.Chem. / Year: 1979
Title: Metal-Free Southern Bean Mosaic Virus Crystals
Authors: Rayment, I. / Johnson, J.E. / Rossmann, M.G.
#7: Journal: Virology / Year: 1978
Title: The Structure of Southern Bean Mosaic Virus at 5 Angstroms Resolution
Authors: Suck, D. / Rayment, I. / Johnson, J.E. / Rossmann, M.G.
#8: Journal: Acta Crystallogr.,Sect.B / Year: 1978
Title: An 11 Angstroms-Resolution Electron Density Map of Southern Bean Mosaic Virus
Authors: Rayment, I. / Johnson, J.E. / Suck, D. / Akimoto, T. / Rossmann, M.G. / Lonberg-Holm, K. / Korant, B.D.
#9: Journal: Virology / Year: 1976
Title: The Structure of Southern Bean Mosaic Virus at 22.5 Angstroms Resolution
Authors: Johnson, J.E. / Akimoto, T. / Suck, D. / Rayment, I. / Rossmann, M.G.
History
DepositionApr 1, 1985Processing site: BNL
SupersessionJul 17, 1985ID: 3SBV
Revision 1.0Jul 17, 1985Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 21, 2012Group: Advisory
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_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _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][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.oper_expression / _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_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.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_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation
Revision 2.1Jun 28, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
B: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
C: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9056
Polymers84,7853
Non-polymers1203
Water61334
1
A: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
B: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
C: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,094,316360
Polymers5,087,102180
Non-polymers7,214180
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: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
B: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
C: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 425 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)424,52630
Polymers423,92515
Non-polymers60115
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
B: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
C: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 509 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)509,43236
Polymers508,71018
Non-polymers72118
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: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
B: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
C: SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.27 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,273,57990
Polymers1,271,77545
Non-polymers1,80445
Water81145
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)334.300, 334.300, 757.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.64549667, 0.57735093), (0.86602536, 0.37267832, -0.33333297), (0.66666704, 0.74535566)
3generate(-0.30901699, -0.17841013, 0.93417257), (0.75576185, -0.64234946, 0.12732297), (0.5773495, 0.74535695, 0.33333247)
4generate(-0.30901699, 0.75576191, 0.57734954), (-0.17841012, -0.64234946, 0.74535695), (0.9341725, 0.12732297, 0.33333247)
5generate(0.5, 0.86602543), (-0.64549663, 0.37267832, 0.66666703), (0.57735088, -0.33333296, 0.74535566)
6generate(0.93417204, -0.35682303), (-0.356823, -0.33333407, -0.87267733), (-0.93417197, 0.12732266, 0.33333407)
7generate(0.80901699, 0.11026352, -0.5773504), (-0.46708651, -0.47568354, -0.74535584), (-0.35682162, 0.87267813, -0.33333346)
8generate(0.5, -0.86602543), (-0.64549663, -0.37267832, -0.66666703), (0.57735088, 0.33333296, -0.74535566)
9generate(-0.5, -0.64549667, 0.57735093), (-0.64549663, -0.16666815, -0.74535615), (0.57735088, -0.74535615, -0.33333185)
10generate(-0.80901699, 0.46708655, 0.35682164), (-0.46708651, -0.14235205, -0.87267752), (-0.35682162, -0.87267752, 0.33333506)

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Components

#1: Protein SOUTHERN BEAN MOSAIC VIRUS COAT PROTEIN


Mass: 28261.676 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Southern bean mosaic virus / Genus: Sobemovirus / Strain: COW PEA STRAIN / References: UniProt: P03607
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.56 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 298615 / % possible obs: 90 % / Observed criterion σ(F): 1

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Processing

RefinementRfactor Rwork: 0.254 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4686 0 3 34 4723
Refinement
*PLUS
Lowest resolution: 14 Å / Highest resolution: 2.8 Å / Num. reflection obs: 141979 / Rfactor obs: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.7 Å2

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