[English] 日本語
Yorodumi
- PDB-2e6w: Solution structure and calcium binding properties of EF-hands 3 a... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2e6w
TitleSolution structure and calcium binding properties of EF-hands 3 and 4 of calsenilin
ComponentsCalsenilin
KeywordsMETAL BINDING PROTEIN / Calcium-bound form
Function / homology
Function and homology information


Phase 1 - inactivation of fast Na+ channels / voltage-gated ion channel activity / regulation of potassium ion transmembrane transport / potassium channel regulator activity / potassium channel activity / axon terminus / voltage-gated potassium channel complex / protein localization to plasma membrane / DNA-binding transcription repressor activity, RNA polymerase II-specific / intracellular protein transport ...Phase 1 - inactivation of fast Na+ channels / voltage-gated ion channel activity / regulation of potassium ion transmembrane transport / potassium channel regulator activity / potassium channel activity / axon terminus / voltage-gated potassium channel complex / protein localization to plasma membrane / DNA-binding transcription repressor activity, RNA polymerase II-specific / intracellular protein transport / transcription corepressor activity / protein-DNA complex / ion channel binding / RNA polymerase II proximal promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase II / dendrite / apoptotic process / calcium ion binding / endoplasmic reticulum / Golgi apparatus / signal transduction / DNA binding / plasma membrane / nucleus / cytosol
EF hand / EF-hand calcium-binding domain profile. / EF-hand calcium-binding domain. / EF-hand domain pair / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand domain pair / EF-hand domain
Calsenilin
Specimen sourceHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsYu, L. / Sun, C. / Mendoza, R. / Hebert, E. / Pereda-Lopez, A. / Hajduk, P.J. / Olejniczak, E.T.
CitationJournal: Protein Sci. / Year: 2007
Title: Solution structure and calcium-binding properties of EF-hands 3 and 4 of calsenilin.
Authors: Yu, L. / Sun, C. / Mendoza, R. / Wang, J. / Matayoshi, E.D. / Hebert, E. / Pereda-Lopez, A. / Hajduk, P.J. / Olejniczak, E.T.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 5, 2007 / Release: Nov 27, 2007
RevisionDateData content typeGroupProviderType
1.0Nov 27, 2007Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calsenilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8893
Polyers11,8081
Non-polymers802
Water0
NMR ensembles
Datacriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

-
Components

#1: Protein/peptide Calsenilin / DRE-antagonist modulator / DREAM / Kv channel-interacting protein 3 / KChIP3 / A-type potassium channel modulatory protein 3


Mass: 11808.465 Da / Num. of mol.: 1 / Fragment: EF-hands 3 and 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: DREAM, KCHIP3 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2W7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1

Experiment-IDSolution-IDType
113D 13C-separated NOESY
223D 15N-separated NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM Calsenilin, 25mM Tris-HCl, 5mM DTT, 15mM CaCl2; 90% H2O, 10% D2O90% H2O/10% D2O
21.0mM Calsenilin, 25mM Tris-HCl, 5mM DTT, 15mM CaCl2; 100% D2O100% D2O
sample conditionspH: 8.0 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer

Manufacturer: Bruker / Model: DRX / Type: Bruker DRX

Field strength (MHz)Spectrometer-ID
5001
8002

-
Processing

NMR software

Developer: A.T.Brunger at al. / Name: CNX / Version: 2000

Classification
structure solution
refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
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