[English] 日本語
Yorodumi
- PDB-6l87: Solution structure of the tandem PWWP-ARID domains of human RBBP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l87
TitleSolution structure of the tandem PWWP-ARID domains of human RBBP1
ComponentsAT-rich interactive domain-containing protein 4A
KeywordsGENE REGULATION / DNA binding / PWWP / ARID
Function / homology
Function and homology information


establishment of Sertoli cell barrier / genomic imprinting / negative regulation of stem cell population maintenance / erythrocyte development / : / positive regulation of stem cell population maintenance / 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 / erythrocyte development / : / positive regulation of stem cell population maintenance / 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 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
AT-rich interactive domain-containing protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGong, W.B. / Perrett, S. / Feng, Y.G.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural insight into chromatin recognition by multiple domains of the tumor suppressor RBBP1.
Authors: Gong, W. / Liang, Q. / Tong, Y. / Perrett, S. / Feng, Y.
History
DepositionNov 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

-
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)26,6041
Polymers26,6041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13430 Å2
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: 26604.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID4A, RBBP1, RBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29374
Sequence detailsRefer to Biomolecular NMR assignments, 13, 177-181

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
171isotropic23D HN(CA)CB
161isotropic23D CBCA(CO)NH
191isotropic23D HNCO
1131isotropic23D HNCA
1121isotropic23D HN(CA)CO
181isotropic23D HN(CO)CA
1111isotropic23D (H)CCH-TOCSY
1141isotropic23D CCH-TOCSY
1101isotropic23D C(CO)NH
142anisotropic22D 1H-15N HSQC
152anisotropic32D 1H-15N HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM sodium phosphate, 700 mM sodium chloride, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O15N/13C_sample90% H2O/10% D2O
solution210 mM sodium phosphate, 700 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
700 mMsodium chloridenatural abundance1
1 mMEDTAnatural abundance1
1 mMDTTnatural abundance1
10 mMsodium phosphatenatural abundance2
700 mMsodium chloridenatural abundance2
1 mMEDTAnatural abundance2
Sample conditionsIonic strength: 720 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 302 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II9501
Bruker AVANCE IIBrukerAVANCE II6002
Varian DDIIVarianDDII6003

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: 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

+
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