[English] 日本語
Yorodumi
- PDB-1cey: ASSIGNMENTS, SECONDARY STRUCTURE, GLOBAL FOLD, AND DYNAMICS OF CH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cey
TitleASSIGNMENTS, SECONDARY STRUCTURE, GLOBAL FOLD, AND DYNAMICS OF CHEMOTAXIS Y PROTEIN USING THREE-AND FOUR-DIMENSIONAL HETERONUCLEAR (13C,15N) NMR SPECTROSCOPY
ComponentsCHEY
KeywordsSIGNAL TRANSDUCTION
Function / homology
Function and homology information


bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity ...bacterial-type flagellum basal body, C ring / bacterial-type flagellum rotor complex / bacterial-type flagellum-dependent swimming motility / regulation of bacterial-type flagellum-dependent cell motility / aerotaxis / bacterial-type flagellum / regulation of chemotaxis / thermotaxis / internal peptidyl-lysine acetylation / phosphorelay response regulator activity / protein acetylation / acetyltransferase activity / phosphorelay signal transduction system / chemotaxis / magnesium ion binding / signal transduction / cytosol / cytoplasm
Similarity search - Function
Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chemotaxis protein CheY / Chemotaxis protein CheY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR
AuthorsMoy, F.J. / Lowry, D.F. / Matsumura, P. / Dahlquist, F.W. / Krywko, J.E. / Domaille, P.J.
CitationJournal: Biochemistry / Year: 1994
Title: Assignments, secondary structure, global fold, and dynamics of chemotaxis Y protein using three- and four-dimensional heteronuclear (13C,15N) NMR spectroscopy.
Authors: Moy, F.J. / Lowry, D.F. / Matsumura, P. / Dahlquist, F.W. / Krywko, J.E. / Domaille, P.J.
History
DepositionNov 23, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHEY


Theoretical massNumber of molelcules
Total (without water)13,9811
Polymers13,9811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: CIS PROLINE - PRO 110 MODEL 1 / 2: CIS PROLINE - PRO 110 MODEL 2 / 3: CIS PROLINE - PRO 110 MODEL 3 / 4: CIS PROLINE - PRO 110 MODEL 4 / 5: CIS PROLINE - PRO 110 MODEL 5 / 6: CIS PROLINE - PRO 110 MODEL 6 / 7: CIS PROLINE - PRO 110 MODEL 7 / 8: CIS PROLINE - PRO 110 MODEL 8 / 9: CIS PROLINE - PRO 110 MODEL 9 / 10: CIS PROLINE - PRO 110 MODEL 10 / 11: CIS PROLINE - PRO 110 MODEL 11 / 12: CIS PROLINE - PRO 110 MODEL 12 / 13: CIS PROLINE - PRO 110 MODEL 13 / 14: CIS PROLINE - PRO 110 MODEL 14 / 15: CIS PROLINE - PRO 110 MODEL 15 / 16: CIS PROLINE - PRO 110 MODEL 16 / 17: CIS PROLINE - PRO 110 MODEL 17 / 18: CIS PROLINE - PRO 110 MODEL 18 / 19: CIS PROLINE - PRO 110 MODEL 19 / 20: CIS PROLINE - PRO 110 MODEL 20 / 21: CIS PROLINE - PRO 110 MODEL 21 / 22: CIS PROLINE - PRO 110 MODEL 22 / 23: CIS PROLINE - PRO 110 MODEL 23 / 24: CIS PROLINE - PRO 110 MODEL 24 / 25: CIS PROLINE - PRO 110 MODEL 25 / 26: CIS PROLINE - PRO 110 MODEL 26 / 27: CIS PROLINE - PRO 110 MODEL 27 / 28: CIS PROLINE - PRO 110 MODEL 28 / 29: CIS PROLINE - PRO 110 MODEL 29 / 30: CIS PROLINE - PRO 110 MODEL 30 / 31: CIS PROLINE - PRO 110 MODEL 31 / 32: CIS PROLINE - PRO 110 MODEL 32 / 33: CIS PROLINE - PRO 110 MODEL 33 / 34: CIS PROLINE - PRO 110 MODEL 34 / 35: CIS PROLINE - PRO 110 MODEL 35 / 36: CIS PROLINE - PRO 110 MODEL 36 / 37: CIS PROLINE - PRO 110 MODEL 37 / 38: CIS PROLINE - PRO 110 MODEL 38 / 39: CIS PROLINE - PRO 110 MODEL 39 / 40: CIS PROLINE - PRO 110 MODEL 40 / 41: CIS PROLINE - PRO 110 MODEL 41 / 42: CIS PROLINE - PRO 110 MODEL 42 / 43: CIS PROLINE - PRO 110 MODEL 43 / 44: CIS PROLINE - PRO 110 MODEL 44 / 45: CIS PROLINE - PRO 110 MODEL 45 / 46: CIS PROLINE - PRO 110 MODEL 46
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)46 / -
Representative

-
Components

#1: Protein CHEY


Mass: 13981.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: CHEY / References: UniProt: P06143, UniProt: P0AE67*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 46

+
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