[English] 日本語
Yorodumi
- PDB-2wbh: Icosahedral particle of covalent coat protein dimer of bacterioph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wbh
TitleIcosahedral particle of covalent coat protein dimer of bacteriophage MS2
ComponentsCOAT PROTEIN
KeywordsVIRUS / CAPSID PROTEIN / COVALENT DIMER / VIRION / RNA-BINDING
Function / homology
Function and homology information


negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid
Similarity search - Domain/homology
Biological speciesENTEROBACTERIA PHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 Å
AuthorsPlevka, P. / Tars, K. / Liljas, L.
CitationJournal: Protein Sci. / Year: 2009
Title: Structure and Stability of Icosahedral Particles of a Covalent Coat Protein Dimer of Bacteriophage MS2.
Authors: Plevka, P. / Tars, K. / Liljas, L.
History
DepositionFeb 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Refinement description / Version format compliance
Revision 1.2Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)82,1163
Polymers82,1163
Non-polymers00
Water00
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)4,926,938180
Polymers4,926,938180
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: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 5


  • icosahedral pentamer
  • 411 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)410,57815
Polymers410,57815
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 493 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)492,69418
Polymers492,69418
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
Unit cell
Length a, b, c (Å)368.200, 368.200, 368.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.485628, -0.246072, 0.838817), (0.730527, 0.641239, -0.234823), (-0.480099, 0.726815, 0.491167)80.33688, -159.59705, 136.43258
3generate(-0.346643, 0.332374, 0.877135), (0.935946, 0.060752, 0.346864), (0.062001, 0.941189, -0.332143)273.06512, -235.28614, 48.87647
4generate(-0.346643, 0.935946, 0.062001), (0.332374, 0.060752, 0.941189), (0.877135, 0.346864, -0.332143)311.84083, -122.46751, -141.66876
5generate(0.485628, 0.730527, -0.480099), (-0.246072, 0.641239, 0.726815), (0.838817, -0.234823, 0.491167)143.07731, 22.94732, -171.87608
6generate(-0.94101, 0.332714, 0.061661), (0.332714, 0.876557, 0.347777), (0.061661, 0.347777, -0.935547)641.80477, -163.70689, 269.33371
7generate(-0.243528, 0.489722, -0.837178), (0.634957, 0.732981, 0.244067), (0.73316, -0.472135, -0.489453)521.51941, -229.42551, 91.14398
8generate(0.641419, -0.234519, -0.730467), (0.72664, 0.491162, 0.480369), (0.246122, -0.838904, 0.485452)309.57866, -262.09805, 158.61772
9generate(0.490865, -0.839133, 0.234323), (0.48106, 0.485286, 0.730123), (-0.726384, -0.245668, 0.641883)298.87743, -216.57217, 378.50851
10generate(-0.48713, -0.488564, 0.723885), (0.2376, 0.723473, 0.648176), (-0.840387, 0.487741, -0.236343)504.20446, -155.76309, 446.93475
11generate(-0.064958, -0.339675, 0.938297), (-0.339675, -0.876605, -0.340858), (0.938297, -0.340858, -0.058436)281.93685, 533.44823, -87.8439
12generate(-0.730163, 0.48014, 0.486135), (-0.641695, -0.72627, -0.246496), (0.234713, -0.491933, 0.838399)458.94369, 599.55937, 33.96323
13generate(-0.237225, 0.840888, -0.486447), (-0.723843, -0.486966, -0.48879), (-0.647901, 0.236158, 0.724191)389.98042, 630.28803, 245.7152
14generate(0.732632, 0.244028, -0.635375), (-0.472593, -0.489404, -0.732898), (-0.489803, 0.837218, -0.243227)170.35193, 583.16826, 254.77799
15generate(0.839098, -0.4856, 0.245166), (-0.235164, -0.730215, -0.64147), (0.490522, 0.480603, -0.726918)103.57733, 523.31798, 48.62713
16generate(0.005968, 0.006961, -0.999958), (0.006961, -0.999952, -0.00692), (-0.999958, -0.00692, -0.006016)548.56837, 367.14512, 554.42152
17generate(0.488063, -0.723789, -0.487774), (-0.723789, -0.647951, 0.237252), (-0.487774, 0.237252, -0.840112)411.50999, 526.34966, 474.37154
18generate(-0.057551, -0.938743, 0.339779), (-0.938743, -0.064948, -0.338443), (0.339779, -0.338443, -0.8775)499.68578, 603.98262, 282.70194
19generate(-0.876853, -0.34084, 0.339051), (-0.34084, -0.056634, -0.938414), (0.339051, -0.938414, -0.066512)691.23979, 492.75789, 244.29359
20generate(-0.837596, 0.243637, -0.488952), (0.243637, -0.634498, -0.733521), (-0.488952, -0.733521, 0.472094)721.45089, 346.38427, 412.22552

-
Components

#1: Protein COAT PROTEIN / ICOSAHEDRAL PARTICLE OF BACTERIOPHAGE MS2 COVALENT COAT PROTEIN DIMER


Mass: 27371.877 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-130,2 AND 4-130
Source method: isolated from a genetically manipulated source
Details: COVALENT DIMER OF MS2 COAT PROTEIN SUBUNITS, SERINE 2 OF SECOND SUBUNIT IS DELETED
Source: (gene. exp.) ENTEROBACTERIA PHAGE MS2 (virus) / Plasmid: PBAD / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): TOP 10 / References: UniProt: P03612
Sequence detailsCOVALENT DIMER OF MS2 COAT PROTEIN SUBUNITS, SERINE 2 OF SECOND SUBUNIT IS DELETED

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.6 Å3/Da / Density % sol: 70.8 % / Description: NONE
Crystal growpH: 9 / Details: 0.1M BICINE PH 9.0, 20% PEG 5000-MONOETHYL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9814
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 10, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 4.7→50 Å / Num. obs: 72743 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 2.9
Reflection shellResolution: 4.7→4.91 Å / Redundancy: 2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.6 / % possible all: 51

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 4.7→50 Å / σ(F): 0 / Stereochemistry target values: RESIDUAL
RfactorNum. reflection% reflection
Rwork0.318 --
obs0.318 72743 84 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.99 Å2 / ksol: 0.8 e/Å3
Displacement parametersBiso mean: 105.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.78 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 4.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 0 0 2892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg3.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 4.7→4.91 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.365 5251 -
obs--51 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

+
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