[English] 日本語
Yorodumi
- PDB-1c7v: NMR SOLUTION STRUCTURE OF THE CALCIUM-BOUND C-TERMINAL DOMAIN (W8... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c7v
TitleNMR SOLUTION STRUCTURE OF THE CALCIUM-BOUND C-TERMINAL DOMAIN (W81-S161) OF CALCIUM VECTOR PROTEIN FROM AMPHIOXUS
ComponentsCALCIUM VECTOR PROTEIN
KeywordsMETAL BINDING PROTEIN / EF-HAND FAMILY / CALCIUM BINDING PROTEIN
Function / homology
Function and homology information


cytoskeletal motor regulator activity / actomyosin structure organization / locomotion / myosin II complex / myosin heavy chain binding / mitotic cytokinesis / post-embryonic development / calcium ion binding / cytoplasm
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calcium vector protein
Similarity search - Component
Biological speciesBranchiostoma lanceolatum (amphioxus)
MethodSOLUTION NMR / Distance Geometry (DGII), Simulated Annealing (Discover)
AuthorsTheret, I. / Baladi, S. / Cox, J.A. / Sakamoto, H. / Craescu, C.T.
CitationJournal: Biochemistry / Year: 2000
Title: Sequential calcium binding to the regulatory domain of calcium vector protein reveals functional asymmetry and a novel mode of structural rearrangement.
Authors: Theret, I. / Baladi, S. / Cox, J.A. / Sakamoto, H. / Craescu, C.T.
History
DepositionMar 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALCIUM VECTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,2791
Polymers9,2791
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)20 / 100agreement with NOE restraints, geometry quality
Representative

-
Components

#1: Protein CALCIUM VECTOR PROTEIN / CAVP


Mass: 9279.268 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RESIDUES 81-161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Branchiostoma lanceolatum (amphioxus) / Tissue: MUSCLE / Plasmid: PET24A / Production host: Escherichia coli (E. coli) / References: UniProt: P04573

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D (1H-15N)NOESY-HSQC
NMR detailsText: This structure was determined using 2D, homonuclear and 3D heteronuclear experiments.

-
Sample preparation

Details
Solution-IDContentsSolvent system
1UnlabeledDeuterated Tris buffer (20 mM), 100 mM KCl, pH 6.5, 7% D2O
2Uniformly 15N labeledDeuterated Tris buffer (20 mM), 100 mM KCl, pH 6.5
Sample conditionsIonic strength: 100 mM KCl / pH: 6.5 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian Unity 500 / Manufacturer: Varian / Model: Unity 500 / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Felix97MSI (San Diego)structure solution
Felix97MSI (San Diego)refinement
RefinementMethod: Distance Geometry (DGII), Simulated Annealing (Discover)
Software ordinal: 1
Details: The structure is based on 938 NOE restraints, 66 hydrogen bond restraints and 99 dihedral angle restraints
NMR ensembleConformer selection criteria: agreement with NOE restraints, geometry quality
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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