[English] 日本語
Yorodumi
- PDB-2cka: Solution structures of the BRK domains of the human Chromo Helica... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cka
TitleSolution structures of the BRK domains of the human Chromo Helicase Domain 7 and 8, reveals structural similarity with GYF domain suggesting a role in protein interaction
ComponentsCHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8
KeywordsHYDROLASE / BRK DOMAIN / TRANSCRIPTION ELONGATION / CHROMATIN REMODELING / PROTEIN-PROTEIN INTERACTION / TRANSCRIPTION / HELICASE / NUCLEAR PROTEIN / CHROMATIN REGULATOR
Function / homology
Function and homology information


digestive tract development / negative regulation of fibroblast apoptotic process / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / social behavior / MLL1 complex / prepulse inhibition / methylated histone binding / DNA helicase activity / Deactivation of the beta-catenin transactivating complex ...digestive tract development / negative regulation of fibroblast apoptotic process / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / social behavior / MLL1 complex / prepulse inhibition / methylated histone binding / DNA helicase activity / Deactivation of the beta-catenin transactivating complex / brain development / negative regulation of canonical Wnt signaling pathway / mRNA processing / beta-catenin binding / Wnt signaling pathway / p53 binding / histone binding / DNA helicase / in utero embryonic development / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 8 / Ribosomal Protein L9; domain 1 - #120 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Ribosomal Protein L9; domain 1 / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromodomain-helicase-DNA-binding protein 8 / Ribosomal Protein L9; domain 1 - #120 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Ribosomal Protein L9; domain 1 / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CANDID IN CYANA
AuthorsAb, E. / de Jong, R.N. / Diercks, T. / Xiaoyun, J. / Daniels, M. / Kaptein, R. / Folkers, G.E.
CitationJournal: To be Published
Title: Solution Structures of the Brk Domains of the Human Chromo Helicase Domain 7 and 8, Reveals Structural Similarity with Gyf Domain Suggesting a Role in Protein Interaction
Authors: Ab, E. / De Jong, R.N. / Diercks, T. / Xiaoyun, J. / Daniels, M. / Kaptein, R. / Folkers, G.E.
History
DepositionApr 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8


Theoretical massNumber of molelcules
Total (without water)11,0601
Polymers11,0601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8 / ATP-DEPENDENT HELICASE CHD8 / CHD-8 / HELICASE WITH SNF2 DOMAIN 1


Mass: 11059.638 Da / Num. of mol.: 1 / Fragment: BRK DOMAIN, RESIDUES 2012-2085
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: SELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA CELL LINES
Plasmid: PHISLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q9HCK8, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HN(CA)CO
131HN(CA)CB
141CBCA(CO)NH
151HBHA(CO)NH
161HNCAHA
171CC(CO)NH
181CCH-COSY
191(H)CCH- TOCSY
1101HNH-NOESY
1111HCH- NOESY
1121CNH-NOESY
1131HH- NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED CHD8 2012-2085

-
Sample preparation

DetailsContents: 95% H2O/5% D2O
Sample conditionsIonic strength: 150 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementMethod: CANDID IN CYANA / Software ordinal: 1
Details: EFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / 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://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