[English] 日本語
Yorodumi
- PDB-2cpb: SOLUTION NMR STRUCTURES OF THE MAJOR COAT PROTEIN OF FILAMENTOUS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cpb
TitleSOLUTION NMR STRUCTURES OF THE MAJOR COAT PROTEIN OF FILAMENTOUS BACTERIOPHAGE M13 SOLUBILIZED IN DODECYLPHOSPHOCHOLINE MICELLES, 25 LOWEST ENERGY STRUCTURES
ComponentsM13 MAJOR COAT PROTEIN
KeywordsVIRAL PROTEIN / MAJOR COAT PROTEIN / BACTERIOPHAGE M13 / ASSEMBLY / MICELLE / MEMBRANE
Function / homology
Function and homology information


helical viral capsid / host cell plasma membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #80 / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage M13 (virus)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING, THIS VERSION OF X-PLOR WAS EXTENDED FOR FLOATING CHIRALITY
AuthorsPapavoine, C.H.M. / Christiaans, B.E.C. / Folmer, R.H.A. / Konings, R.N.H. / Hilbers, C.W.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Solution structure of the M13 major coat protein in detergent micelles: a basis for a model of phage assembly involving specific residues.
Authors: Papavoine, C.H. / Christiaans, B.E. / Folmer, R.H. / Konings, R.N. / Hilbers, C.W.
#1: Journal: Biochemistry / Year: 1997
Title: Backbone Dynamics of the Major Coat Protein of Bacteriophage M13 in Detergent Micelles by 15N Nuclear Magnetic Resonance Relaxation Measurements Using the Model-Free Approach and Reduced Spectral Density Mapping
Authors: Papavoine, C.H. / Remerowski, M.L. / Horstink, L.M. / Konings, R.N. / Hilbers, C.W. / Van De Ven, F.J.
#2: Journal: Eur.J.Biochem. / Year: 1995
Title: NMR Studies of the Major Coat Protein of Bacteriophage M13. Structural Information of Gviiip in Dodecylphosphocholine Micelles
Authors: Papavoine, C.H. / Aelen, J.M. / Konings, R.N. / Hilbers, C.W. / Van De Ven, F.J.
#3: Journal: Biochemistry / Year: 1994
Title: Location of M13 Coat Protein in Sodium Dodecyl Sulfate Micelles as Determined by NMR
Authors: Papavoine, C.H. / Konings, R.N. / Hilbers, C.W. / Van De Ven, F.J.
#4: Journal: Biochemistry / Year: 1993
Title: Assignment of 1H, 15N, and Backbone 13C Resonances in Detergent-Solubilized M13 Coat Protein Via Multinuclear Multidimensional NMR: A Model for the Coat Protein Monomer
Authors: Van De Ven, F.J. / Van Os, J.W. / Aelen, J.M. / Wymenga, S.S. / Remerowski, M.L. / Konings, R.N. / Hilbers, C.W.
History
DepositionApr 16, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M13 MAJOR COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)5,2431
Polymers5,2431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 80LOWEST ENERGY, DISTANCE RESTRAINTS SMALLER THAN 0.5 A, DIHEDRAL VIOLATIONS SMALLER THAN 5 DEGREES
Representative

-
Components

#1: Protein/peptide M13 MAJOR COAT PROTEIN / M13 GENE-VIII-PROTEIN OR M13 GVIIIP


Mass: 5243.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage M13 (virus) / Genus: Inovirus / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P69541

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131NOESY
141NOESY-HMQC (15N AND 13C)
151TOCSY-HMQC (15N)
161(H)CCH-TOCSY
171HMQC-J
181HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N -LABELED M13 COAT PROTEIN SOLUBILIZED IN DEUTERATED DODECYLPHOSPHOCHOLINE MICELLES (CONCENTRATION COAT/DODPCHO = 1:200)

-
Sample preparation

DetailsContents: H2O
Sample conditionspH: 4.9 / Temperature: 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY4001
Bruker AMBrukerAM5002
Bruker AMXBrukerAMX6003

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING, THIS VERSION OF X-PLOR WAS EXTENDED FOR FLOATING CHIRALITY
Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY, DISTANCE RESTRAINTS SMALLER THAN 0.5 A, DIHEDRAL VIOLATIONS SMALLER THAN 5 DEGREES
Conformers calculated total number: 80 / Conformers submitted total number: 25

+
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