[English] 日本語
Yorodumi
- PDB-2aqf: Structural and functional analysis of ADA2 alpha swirm domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aqf
TitleStructural and functional analysis of ADA2 alpha swirm domain
Componentstranscriptional adaptor 2, Ada2 alpha
KeywordsTRANSCRIPTION / helix-turn-helix
Function / homology
Function and homology information


Formation of WDR5-containing histone-modifying complexes / SAGA-type complex / ATAC complex / SAGA complex / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / regulation of protein phosphorylation / regulation of protein stability / mitotic spindle ...Formation of WDR5-containing histone-modifying complexes / SAGA-type complex / ATAC complex / SAGA complex / regulation of tubulin deacetylation / regulation of cell division / regulation of embryonic development / regulation of protein phosphorylation / regulation of protein stability / mitotic spindle / chromatin organization / mitotic cell cycle / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus
Similarity search - Function
Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / Transcriptional adapter 2-alpha-like domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Myb domain / Zinc finger, ZZ-type ...Transcriptional adaptor 2 / ADA2-like, zinc finger, ZZ-type / Transcriptional adapter 2-alpha-like domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Myb domain / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Transcriptional adapter 2-alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics
AuthorsQian, C. / Zhang, Q. / Zhou, M.-M. / Zeng, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structure and chromosomal DNA binding of the SWIRM domain.
Authors: Qian, C. / Zhang, Q. / Li, S. / Zeng, L. / Walsh, M.J. / Zhou, M.M.
History
DepositionAug 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: transcriptional adaptor 2, Ada2 alpha


Theoretical massNumber of molelcules
Total (without water)10,0431
Polymers10,0431
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)1 / 100structure with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein transcriptional adaptor 2, Ada2 alpha


Mass: 10042.671 Da / Num. of mol.: 1 / Fragment: swirm domain, residues 355-443
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tada21 / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 27369796, UniProt: Q8CHV6*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 13C-separated NOESY
121HACA
131HN(CO)CA
141HN(CA)CB
151HN(CO)CACB
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM ada2 alpha swirm domain, U-15N, 13C, 50mM phosphate buffer, 100mm NaCl, pH 6.5, 90% H2O, 10% D2O90% H2O/10% D2O
21mM ada2 alpha swirm domain, U-15N, 13C, 50mM phosphate buffer, 100mm NaCl, pH 6.5, 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipeBaxprocessing
CNS1.1Brunger et alrefinement
NMRView5Johnsondata analysis
ARIA1.2Nigles, Mrefinement
RefinementMethod: simulated annealing torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structure with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

+
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