[English] 日本語
Yorodumi
- PDB-2lcc: Solution structure of RBBP1 chromobarrel domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lcc
TitleSolution structure of RBBP1 chromobarrel domain
ComponentsAT-rich interactive domain-containing protein 4A
KeywordsTRANSCRIPTION / chromobarrel domain / RBBP1
Function / homology
Function and homology information


establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / : / positive regulation of stem cell population maintenance / erythrocyte development / transcription repressor complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway ...establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / : / positive regulation of stem cell population maintenance / erythrocyte development / transcription repressor complex / negative regulation of cell migration / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / spermatogenesis / Potential therapeutics for SARS / transcription by RNA polymerase II / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
: / : / RBB1NT / RBB1NT (NUC162) domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain ...: / : / RBB1NT / RBB1NT (NUC162) domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / 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 / Tudor domain / Tudor domain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsGong, W. / Feng, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural insight into recognition of methylated histone tails by retinoblastoma-binding protein 1.
Authors: Gong, W. / Zhou, T. / Mo, J. / Perrett, S. / Wang, J. / Feng, Y.
History
DepositionApr 28, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 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 4A


Theoretical massNumber of molelcules
Total (without water)9,0821
Polymers9,0821
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein AT-rich interactive domain-containing protein 4A / ARID domain-containing protein 4A / Retinoblastoma-binding protein 1 / RBBP-1


Mass: 9082.257 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 568-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID4A, RBBP1, RBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P29374

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1322D 1H-13C HSQC aromatic
1423D CBCA(CO)NH
1523D HN(CA)CB
1613D 1H-15N NOESY
1723D 1H-13C NOESY
1813D 1H-15N TOCSY
1913D HBHA(CO)NH
11023D 1H-13C NOESY aromatic
11123D HCACO
11223D HNCO

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-95% 15N] entity-1, 50 mM sodium phosphate-2, 50 mM sodium chloride-3, 5 mM DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-95% 13C; U-95% 15N] entity-5, 50 mM sodium phosphate-6, 50 mM sodium chloride-7, 5 mM DTT-8, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-95% 15N]1
50 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMDTT-41
0.5 mMentity-5[U-95% 13C; U-95% 15N]2
50 mMsodium phosphate-62
50 mMsodium chloride-72
5 mMDTT-82
Sample conditionsIonic strength: 0.4 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 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