[English] 日本語
Yorodumi
- PDB-2jul: NMR Structure of DREAM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jul
TitleNMR Structure of DREAM
ComponentsCalsenilin
KeywordsDNA BINDING PROTEIN / EF-hand / calcium / LxxLL / dimer / Alternative splicing / Apoptosis / Cytoplasm / Endoplasmic reticulum / Golgi apparatus / Ion transport / Ionic channel / Lipoprotein / Membrane / Nucleus / Palmitate / Polymorphism / Potassium / Potassium channel / Potassium transport / Repressor / Transcription / Transcription regulation / Transport / Voltage-gated channel
Function / homology
Function and homology information


Phase 1 - inactivation of fast Na+ channels / regulation of potassium ion transmembrane transport / response to pain / behavioral response to pain / response to magnesium ion / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / core promoter sequence-specific DNA binding / regulation of neuron apoptotic process ...Phase 1 - inactivation of fast Na+ channels / regulation of potassium ion transmembrane transport / response to pain / behavioral response to pain / response to magnesium ion / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / core promoter sequence-specific DNA binding / regulation of neuron apoptotic process / axon terminus / sensory perception of pain / molecular function activator activity / protein localization to plasma membrane / protein-DNA complex / intracellular protein transport / potassium ion transport / DNA-binding transcription repressor activity, RNA polymerase II-specific / calcium-dependent protein binding / sequence-specific DNA binding / transmembrane transporter binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / negative regulation of DNA-templated transcription / dendrite / calcium ion binding / apoptotic process / Golgi apparatus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / endoplasmic reticulum / DNA binding / nucleus / cytosol
Similarity search - Function
Recoverin family / EF-hand domain pair / 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 ...Recoverin family / EF-hand domain pair / 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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsAmes, J.
CitationJournal: Biochemistry / Year: 2008
Title: NMR structure of DREAM: Implications for Ca(2+)-dependent DNA binding and protein dimerization.
Authors: Lusin, J.D. / Vanarotti, M. / Li, C. / Valiveti, A. / Ames, J.B.
History
DepositionAug 30, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calsenilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5803
Polymers29,5001
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

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


Mass: 29499.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kcnip3, Csen, Dream, Kchip3 / Plasmid: pET23a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9QXT8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D 1H-13C NOESY
1713D (H)CCH-TOCSY

-
Sample preparation

DetailsContents: 0.5 mM [U-13C; U-15N] protein, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: entity_1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 20 mM / pH: 7.4 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, F. et al.processing
X-PLOR3.1Brunger, A.T. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

+
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