[English] 日本語
Yorodumi
- PDB-2b2g: MS2 Wild-type RNA stemloop complexed with an N87S mutant MS2 capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b2g
TitleMS2 Wild-type RNA stemloop complexed with an N87S mutant MS2 capsid
Components
  • 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
  • Coat protein
KeywordsVIRUS/VIRAL PROTEIN/RNA / CAPSID / COMPLEX (CAPSID PROTEIN - RNA HAIRPIN) / HAIRPIN / LEVIVIRUS / VIRUS/VIRAL / PROTEIN/RNA / VIRUS-VIRAL PROTEIN-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 speciesEnterobacterio phage MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 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
DepositionSep 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)53,2605
Polymers53,2605
Non-polymers00
Water3,225179
1
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,195,578300
Polymers3,195,578300
Non-polymers00
Water5,405300
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
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 5


  • icosahedral pentamer
  • 266 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)266,29825
Polymers266,29825
Non-polymers00
Water45025
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 6


  • icosahedral 23 hexamer
  • 320 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)319,55830
Polymers319,55830
Non-polymers00
Water54030
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
R: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
S: 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'
A: Coat protein
B: Coat protein
C: Coat protein
x 10


  • crystal asymmetric unit, crystal frame
  • 533 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)532,59650
Polymers532,59650
Non-polymers00
Water90150
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)287.450, 287.450, 651.650
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, -0.8660254), (0.64549722, 0.372678, 0.66666667), (-0.57735027, -0.33333333, 0.74535599)
3generate(-0.30901699, -0.75576131, -0.57735027), (0.17841104, -0.64235033, 0.74535599), (-0.93417236, 0.127322, 0.33333333)
4generate(-0.30901699, 0.17841104, -0.93417236), (-0.75576131, -0.64235033, 0.127322), (-0.57735027, 0.74535599, 0.33333333)
5generate(0.5, 0.64549722, -0.57735027), (-0.8660254, 0.372678, -0.33333333), (0.66666667, 0.74535599)
6generate(0.30901699, -0.75576131, -0.57735027), (-0.75576131, -0.563661, 0.33333333), (-0.57735027, 0.33333333, -0.74535599)
7generate(-0.35682209, -0.93417236), (-0.93417236, 0.33333333, -0.127322), (0.35682209, 0.872678, -0.33333333)
8generate(0.30901699, 0.17841104, -0.93417236), (-0.17841104, 0.97568366, 0.127322), (0.93417236, 0.127322, 0.33333333)
9generate(0.80901699, 0.11026409, -0.57735027), (0.46708618, 0.47568366, 0.74535599), (0.35682209, -0.872678, 0.33333333)
10generate(0.80901699, -0.46708618, -0.35682209), (0.11026409, -0.47568366, 0.872678), (-0.57735027, -0.74535599, -0.33333333)

-
Components

#1: RNA chain 5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*UP*GP*U)-3'


Mass: 6062.657 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Coat protein


Mass: 13711.438 Da / Num. of mol.: 3 / Mutation: N87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: MS2 COATPROTEIN in 1.25% or 1.5% PEG 8000, 0.4M SODIUM PHOSPHATE BUFFER, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
20.4M SODIUM PHOSPHATE BUFFER11
3water11
4PEG 800012
50.4M SODIUM PHOSPHATE BUFFER12
6water12

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 201426 / Num. obs: 162584 / % possible obs: 80.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rsym value: 0.193 / Net I/σ(I): 8.2
Reflection shellResolution: 3.02→3.16 Å / Redundancy: 1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.342 / % possible all: 44.4

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 3.02→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B ...Details: The waters listed in remark 525 are ncs symmetry related waters which are in hydrogen bonding distance to protein or RNA when the biological molecule is generated. NCS symmetry related B chain instead of the chain used for the actual refinement has been included so that the protein-RNA interactions between the AB dimer and the R chain RNA are clear without generating the NCS symmetry related 'B' chain.
RfactorNum. reflectionSelection details
Rfree0.209 6510 RANDOM
Rwork0.202 --
obs0.202 162584 -
all-201426 -
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 3.02→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 661 0 179 3726
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.3

+
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