[English] 日本語
Yorodumi
- PDB-4sbv: The REFINEMENT OF SOUTHERN BEAN MOSAIC VIRUS IN RECIPROCAL SPACE -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / calcium ion binding / lipid 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more