[English] 日本語
Yorodumi
- PDB-2bs0: MS2 (N87AE89K mutant) - Variant Qbeta RNA hairpin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bs0
TitleMS2 (N87AE89K mutant) - Variant Qbeta RNA hairpin complex
Components
  • 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
  • COAT PROTEIN
KeywordsVIRUS/RNA / CAPSID / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / HAIRPIN / LEVIVIRUS / VIRUS/VIRAL PROTEIN/RNA / RNA-BINDING / STRUCTURAL PROTEIN / VIRUS COAT PROTEIN / ICOSAHEDRAL VIRUS / VIRUS-RNA complex
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
MS2 Viral Coat Protein / MS2 Viral Coat Protein / Levivirus coat protein / Levivirus coat protein / Bacteriophage RNA-type, capsid / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesBACTERIOPHAGE MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHorn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. ...Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
CitationJournal: Structure / Year: 2006
Title: Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2.
Authors: Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G.
History
DepositionMay 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'


Theoretical massNumber of molelcules
Total (without water)53,8245
Polymers53,8245
Non-polymers00
Water3,387188
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
x 60


Theoretical massNumber of molelcules
Total (without water)3,229,450300
Polymers3,229,450300
Non-polymers00
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
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
x 5


  • icosahedral pentamer
  • 269 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)269,12125
Polymers269,12125
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
x 6


  • icosahedral 23 hexamer
  • 323 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)322,94530
Polymers322,94530
Non-polymers00
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
R: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
S: 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'
x 60


  • crystal asymmetric unit, crystal frame
  • 3.23 MDa, 300 polymers
Theoretical massNumber of molelcules
Total (without water)3,229,450300
Polymers3,229,450300
Non-polymers00
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)274.200, 273.000, 273.900
Angle α, β, γ (deg.)63.06, 62.98, 63.28
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein COAT PROTEIN


Mass: 13695.505 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE MS2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03612
#2: RNA chain 5'-R(*AP*UP*GP*CP*AP*UP*GP*UP*CP*UP *AP*AP*GP*AP*CP*UP*GP*CP*AP*U)-3'


Mass: 6368.823 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE MS2 (virus)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFORMS THE PHAGE SHELL AND BINDS TO THE PHAGE RNA ENGINEERED RESIDUE IN CHAIN A, ASN 87 TO ALA ...FORMS THE PHAGE SHELL AND BINDS TO THE PHAGE RNA ENGINEERED RESIDUE IN CHAIN A, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 89 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 89 TO LYS ENGINEERED RESIDUE IN CHAIN C, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN C, GLU 89 TO LYS
Sequence detailsASN87 MUTATED TO ALA, GLU89 MUTATED TO LYS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDescription: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.44→30 Å / Num. obs: 460526 / % possible obs: 20 % / Observed criterion σ(I): 0 / Redundancy: 1.3 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 6

-
Processing

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

2ms2


Resolution: 2.45→29.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5670249.33 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 4535 1 %RANDOM
Rwork0.245 ---
obs0.245 456509 20.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.497 Å2 / ksol: 0.333826 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.58 Å22.71 Å2-4.49 Å2
2--1.01 Å2-8.29 Å2
3---3.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.45→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 441 0 188 3515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
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: 2.45→2.49 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.493 67 1.1 %
Rwork0.484 6192 -
obs--5.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

+
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