[English] 日本語
Yorodumi
- PDB-7msf: MS2 PROTEIN CAPSID/RNA COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7msf
TitleMS2 PROTEIN CAPSID/RNA COMPLEX
Components
  • 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
  • MS2 PROTEIN CAPSID
KeywordsVirus/RNA / CCAPSID PROTEIN MS2-RNA APTAMER COMPLEX / RNA-PROTEIN COMPLEX / RNA STEM LOOP / BACTERIOPHAGE MS2 / 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 speciesEnterobacterio phage MS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.8 Å
AuthorsRowsell, S. / Stonehouse, N.J. / Convery, M.A. / Adams, C.J. / Ellington, A.D. / Hirao, I. / Peabody, D.S. / Stockley, P.G. / Phillips, S.E.V.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structures of a series of RNA aptamers complexed to the same protein target.
Authors: Rowsell, S. / Stonehouse, N.J. / Convery, M.A. / Adams, C.J. / Ellington, A.D. / Hirao, I. / Peabody, D.S. / Stockley, P.G. / Phillips, S.E.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of an RNA Aptamer-Protein Complex at 2.8 A Resolution
Authors: Convery, M.A. / Rowsell, S. / Stonehouse, N.J. / Ellington, A.D. / Hirao, I. / Murray, J.B. / Peabody, D.S. / Phillips, S.E. / Stockley, P.G.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: The Three-Dimensional Structures of Two Complexes between Recombinant MS2 Capsids and RNA Operator Fragments Reveal Sequence-Specific Protein-RNA Interactions
Authors: Valegard, K. / Murray, J.B. / Stonehouse, N.J. / Van Den Worm, S. / Stockley, P.G. / Liljas, L.
#3: Journal: Nature / Year: 1994
Title: Crystal Structure of an RNA Bacteriophage Coat Protein-Operator Complex
Authors: Valegard, K. / Murray, J.B. / Stockley, P.G. / Stonehouse, N.J. / Liljas, L.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: The Refined Structure of Bacteriophage MS2 at 2.8 A Resolution
Authors: Golmohammadi, R. / Valegard, K. / Fridborg, K. / Liljas, L.
History
DepositionMay 20, 1998Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: 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
R: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
S: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID


Theoretical massNumber of molelcules
Total (without water)50,2175
Polymers50,2175
Non-polymers00
Water1,62190
1
R: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
S: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 60


Theoretical massNumber of molelcules
Total (without water)3,013,015300
Polymers3,013,015300
Non-polymers00
Water4,324240
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(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
S: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 5


  • icosahedral pentamer
  • 251 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)251,08525
Polymers251,08525
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
R: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
S: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 6


  • icosahedral 23 hexamer
  • 301 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)301,30230
Polymers301,30230
Non-polymers00
Water43224
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(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
S: 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3'
A: MS2 PROTEIN CAPSID
B: MS2 PROTEIN CAPSID
C: MS2 PROTEIN CAPSID
x 10


  • crystal asymmetric unit, crystal frame
  • 502 kDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)502,16950
Polymers502,16950
Non-polymers00
Water72140
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation9
Unit cell
Length a, b, c (Å)287.500, 287.500, 652.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Cell settingtrigonal
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, 7.9E-7), (0.6454967, 0.3726783, 0.66666701), (-0.57735086, -0.33333299, 0.74535569)
3generate(-0.30901699, -0.75576184, -0.57734958), (0.17841019, -0.64234953, 0.74535688), (-0.93417252, 0.12732289, 0.33333254)
4generate(-0.30901699, 0.17841019, -0.93417252), (-0.75576184, -0.64234953, 0.12732289), (-0.57734958, 0.74535688, 0.33333254)
5generate(0.5, 0.6454967, -0.57735086), (-0.8660254, 0.3726783, -0.33333299), (7.9E-7, 0.66666701, 0.74535569)
6generate(0.30901699, -0.75576184, -0.57734958), (-0.75576184, -0.5636604, 0.33333317), (-0.57734958, 0.33333317, -0.7453566)
7generate(-0.35682294, -0.93417203), (-0.93417203, 0.33333401, -0.12732261), (0.35682294, 0.87267739, -0.33333401)
8generate(0.30901699, 0.17841019, -0.93417252), (-0.17841019, 0.97568389, 0.12732142), (0.93417252, 0.12732142, 0.3333331)
9generate(0.80901699, 0.11026356, -0.57735037), (0.4670865, 0.47568355, 0.74535586), (0.35682166, -0.87267813, 0.33333345)
10generate(0.80901699, -0.4670865, -0.35682166), (0.11026356, -0.47568355, 0.87267813), (-0.57735037, -0.74535586, -0.33333345)
DetailsTHE COMPLETE PARTICLE CAN BE GENERATED BY APPLYING THE NCS MATRICES TO THE COORDINATES AND THEN APPLYING THE CRYSTALLOGRAPHIC SYMMETRY OPERATORS.

-
Components

#1: RNA chain 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)-3' / F7 / 14-NT RNA APTAMER


Mass: 4500.764 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: FAMILY 7 CONSENSUS SEQUENCE FROM IN VITRO SELECTION
#2: Protein MS2 PROTEIN CAPSID


Mass: 13738.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Gene: COAT PROTEIN / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P03612
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

-
Sample preparation

CrystalDensity % sol: 80 %
Crystal growTemperature: 300 K / pH: 7.4
Details: PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS ...Details: PROTEIN IN 1.25% OR 1.5% PEG 8000, 0.1M NA PHOSPHATE PH 7.4 AND 0.02% NA AZIDE WAS EQUILIBRATED AGAINST 0.35M OR 0.4M NA PHOSPHATE PH 7.4, 0.02% NA AZIDE AT 300 OR 370 C. WASHED CRYSTALS WERE SOAKED IN 2MG/ML RNA.
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2NA3PO411
3NAN311
4NA3PO412
5NAN312
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion, hanging drop / Details: Valegard, K., (1997) J.Mol.Biol., 270, 724.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 mg/mlcapsid1drop
21.25 %(w/v)PEG80001drop
30.1 Msodium phosphate1drop
40.02 %(w/v)sodium azide1drop
50.4 Msodium phosphate1reservoir
60.02 %(w/v)sodium azide1reservoir

-
Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 166584 / % possible obs: 66 % / Redundancy: 1.9 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.192 / Net I/σ(I): 2.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.3 / % possible all: 26
Reflection
*PLUS
% possible obs: 66.4 % / Num. measured all: 317367
Reflection shell
*PLUS
% possible obs: 26.3 %

-
Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.86refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2MS2

2ms2


Resolution: 2.8→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.211 6676 4 %RANDOM
Rwork0.2 ---
all-166564 --
obs-166564 65.9 %-
Displacement parametersBiso mean: 36.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.3 Å
Luzzati d res low-30 Å
Luzzati sigma a0.35 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 533 0 90 3527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.772
X-RAY DIFFRACTIONx_mcangle_it5.782.5
X-RAY DIFFRACTIONx_scbond_it6.12.5
X-RAY DIFFRACTIONx_scangle_it8.213
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 471 4.1 %
Rwork0.321 11134 -
obs--27.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMTOPH19.SOL
X-RAY DIFFRACTION3DNA-RNA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.86 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

+
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