[English] 日本語
Yorodumi
- PDB-2c0x: MOLECULAR STRUCTURE OF FD FILAMENTOUS BACTERIOPHAGE REFINED WITH ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2c0x
TitleMOLECULAR STRUCTURE OF FD FILAMENTOUS BACTERIOPHAGE REFINED WITH RESPECT TO X-RAY FIBRE DIFFRACTION AND SOLID-STATE NMR DATA
ComponentsCOAT PROTEIN B
KeywordsVIRAL PROTEIN / FILAMENTOUS BACTERIOPHAGE / ALPHA-HELIX / MEMBRANE PROTEINS / STRUCTURAL PROTEIN / TRANSMEMBRANE / HELICAL VIRUS
Function / homologyCapsid protein G8P / Bacteriophage M13, G8P, capsid domain superfamily / Phage major coat protein, Gp8 / helical viral capsid / host cell membrane / integral component of membrane / Capsid protein G8P
Function and homology information
Biological speciesENTEROBACTERIA PHAGE FD (virus)
MethodSOLID-STATE NMR
Model type detailsMINIMIZED AVERAGE
AuthorsMarvin, D.A. / Welsh, L.C. / Symmons, M.F. / Scott, W.R.P. / Straus, S.K.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Molecular Structure of Fd (F1, M13) Filamentous Bacteriophage Refined with Respect to X-Ray Fibre Diffraction and Solid-State NMR Data Supports Specific Models of Phage Assembly at the Bacterial Membrane.
Authors: Marvin, D.A. / Welsh, L.C. / Symmons, M.F. / Scott, W.R.P. / Straus, S.K.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Molecular Models and Structural Comparisons of Native and Mutant Class I Filamentous Bacteriophages Ff (Fd, F1, M13), If1 and Ike
Authors: Marvin, D.A. / Hale, R.D. / Nave, C. / Helmer-Citterich, M.
#2: Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
Authors: Marvin, D.A.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Matching Electrostatic Charge between DNA and Coat Protein in Filamentous Bacteriophage. Fibre Diffraction of Charge-Deletion Mutants.
Authors: Symmons, M.F. / Welsh, L.C. / Nave, C. / Marvin, D.A. / Perham, R.N.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure of the Coat Protein in Fd Filamentous Bacteriophage Particles Determined by Solid-State NMR Spectroscopy
Authors: Zeri, A.C. / Mesleh, M.F. / Nevzorov, A.A. / Opella, S.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 23, 2017Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COAT PROTEIN B


Theoretical massNumber of molelcules
Total (without water)5,2121
Polymers5,2121
Non-polymers00
Water0
1
A: COAT PROTEIN B
x 55


Theoretical massNumber of molelcules
Total (without water)286,66155
Polymers286,66155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5555
point symmetry operation50
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1), (-1), (1)-80.75
2generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)-80.75
3generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)-80.75
4generate(0.809017, -0.587785), (0.587785, 0.809017), (1)-80.75
5generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)-80.75
6generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)-64.6
7generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)-64.6
8generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)-64.6
9generate(1), (1), (1)-64.6
10generate(0.309017, -0.951057), (0.951057, 0.309017), (1)-64.6
11generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)-48.45
12generate(-1), (-1), (1)-48.45
13generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)-48.45
14generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)-48.45
15generate(0.809017, -0.587785), (0.587785, 0.809017), (1)-48.45
16generate(0.309017, -0.951057), (0.951057, 0.309017), (1)-32.3
17generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)-32.3
18generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)-32.3
19generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)-32.3
20generate(1), (1), (1)-32.3
21generate(0.809017, -0.587785), (0.587785, 0.809017), (1)-16.15
22generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)-16.15
23generate(-1), (-1), (1)-16.15
24generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)-16.15
25generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)-16.15
26generate(1), (1), (1)
27generate(0.309017, -0.951057), (0.951057, 0.309017), (1)
28generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)
29generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)
30generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)
31generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)16.15
32generate(0.809017, -0.587785), (0.587785, 0.809017), (1)16.15
33generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)16.15
34generate(-1), (-1), (1)16.15
35generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)16.15
36generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)32.3
37generate(1), (1), (1)32.3
38generate(0.309017, -0.951057), (0.951057, 0.309017), (1)32.3
39generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)32.3
40generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)32.3
41generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)48.45
42generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)48.45
43generate(0.809017, -0.587785), (0.587785, 0.809017), (1)48.45
44generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)48.45
45generate(-1), (-1), (1)48.45
46generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)64.6
47generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)64.6
48generate(1), (1), (1)64.6
49generate(0.309017, -0.951057), (0.951057, 0.309017), (1)64.6
50generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)64.6
51generate(-1), (-1), (1)80.75
52generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)80.75
53generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)80.75
54generate(0.809017, -0.587785), (0.587785, 0.809017), (1)80.75
55generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)80.75
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = -36.00 DEGREES RISE PER SUBUNIT (HEIGHT) = 16.15 ANGSTROMS IN ADDITION, THERE IS 5-FOLD CIRCULAR SYMMETRY AROUND THE HELIX AXIS

-
Components

#1: Protein/peptide COAT PROTEIN B / FD GENE 8 COAT PROTEIN / MAJOR COAT PROTEIN


Mass: 5212.021 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE FD (virus)
Description: H. HOFFMANN-BERLING Z. NATURFORSCH. SECT. B BIOSCI.
References: UniProt: P69539
Compound detailsRESIDUE IN CHAIN A, TYR 44 TO MET WAS AN INTENTIONAL MUTATION IN THE VIRAL GENOME, THIS MUTATION IS ...RESIDUE IN CHAIN A, TYR 44 TO MET WAS AN INTENTIONAL MUTATION IN THE VIRAL GENOME, THIS MUTATION IS KNOWN TO IMPROVE ORIENTATION FOR XRAY STUDIES. THE VIRUS WAS THEN GROWN IN THE NORMAL WAY, NOT USING RECOMBINANT METHODS, SEE REFERENCE 1
Sequence detailsY21M MUTANT IN CHAIN

-
Experimental details

-
Experiment

ExperimentMethod: SOLID-STATE NMR

-
Processing

NMR ensembleConformers submitted total number: 1

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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