[English] 日本語
Yorodumi
- PDB-2kk0: Solution structure of dead ringer-like protein 1 (at-rich interac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kk0
TitleSolution structure of dead ringer-like protein 1 (at-rich interactive domain-containing protein 3a) from homo sapiens, northeast structural genomics consortium (NESG) target hr4394c
ComponentsAT-rich interactive domain-containing protein 3A
KeywordsTranscription regulator / Dead Ringer / AT-rich interaction domain / NESG / ARID / Cytoplasm / DNA-binding / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / transcription coregulator activity / membrane raft / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
REKLES domain / AT-rich interactive domain-containing protein 3 / REKLES domain profile. / ARID DNA-binding domain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain ...REKLES domain / AT-rich interactive domain-containing protein 3 / REKLES domain profile. / ARID DNA-binding domain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, distance geometry, simulated annealing
Model detailsfewest violations, model 1
AuthorsLiu, G. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. ...Liu, G. / Wang, D. / Nwosu, C. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2010
Title: Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: a human cancer protein interaction network target.
Authors: Liu, G. / Huang, Y.J. / Xiao, R. / Wang, D. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 14, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 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
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AT-rich interactive domain-containing protein 3A


Theoretical massNumber of molelcules
Total (without water)17,1631
Polymers17,1631
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein AT-rich interactive domain-containing protein 3A / ARID domain-containing protein 3A / Dead ringer-like protein 1 / B-cell regulator of IgH ...ARID domain-containing protein 3A / Dead ringer-like protein 1 / B-cell regulator of IgH transcription / Bright / E2F-binding protein 1


Mass: 17162.664 Da / Num. of mol.: 1 / Fragment: ARID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID3A, DRIL1, DRIL3, DRX, E2FBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99856
Sequence detailsTHE AUTHORS STATE THAT THEIR CONSTRUCT INCLUDES AN 11-RESIDUE N-TERMINAL HEXAHIS PURIFIATION TAG; ...THE AUTHORS STATE THAT THEIR CONSTRUCT INCLUDES AN 11-RESIDUE N-TERMINAL HEXAHIS PURIFIATION TAG; RESIDUE NUMBERS 12 145 CORRESPOND TO RESIDUES 218 TO 351 OF THE FULL-LENGTH HUMAN ARID3 PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB
1623D 1H-13C NOESY
1713D HBHA(CO)NH
1813D H(CCO)NH
1923D (H)CCH-COSY
11013D 1H-13C-15N simutaneous NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.92 mM [U-100% 13C; U-100% 15N] protein 95% H2O/5% D2O95% H2O/5% D2O
20.92 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
30.95 mM [U-10% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.92 mMprotein-1[U-100% 13C; U-100% 15N]1
0.92 mMprotein-2[U-100% 13C; U-100% 15N]2
0.95 mMprotein-3[U-10% 13C; U-100% 15N]3
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
AutoStructure1.2Huang, Tejero, Powers and Montelionerefinement
AutoStructure1.2Huang, Tejero, Powers and Montelionedata analysis
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
XEASY1.3Bartels et al.chemical shift assignment
XEASY1.3Bartels et al.data analysis
XEASY1.3Bartels et al.peak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
VnmrJVariancollection
RefinementMethod: molecular dynamics, distance geometry, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / 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://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