[English] 日本語
Yorodumi
- PDB-2rt5: Structural insights into the recruitment of SMRT by the co-repres... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rt5
TitleStructural insights into the recruitment of SMRT by the co-repressor SHARP under phosphorylative regulation
Components
  • Msx2-interacting protein
  • peptide from Silencing mediator of retinoic acid and thyroid hormone receptor
KeywordsTRANSCRIPTION REGULATOR / SHARP / SPOC domain / SMRT / phosphorylation
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / RHOBTB1 GTPase cycle / positive regulation of neurogenesis / : ...Loss of MECP2 binding ability to the NCoR/SMRT complex / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / negative regulation of androgen receptor signaling pathway / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / Notch binding / RHOBTB1 GTPase cycle / positive regulation of neurogenesis / : / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / Regulation of MECP2 expression and activity / estrous cycle / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / Notch signaling pathway / lactation / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / cerebellum development / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Transcriptional regulation of white adipocyte differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Nuclear Receptor transcription pathway / nuclear matrix / HCMV Early Events / transcription corepressor activity / response to estradiol / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain ...SHARP, RNA recognition motif 1 / SHARP, RNA recognition motif 2 / SHARP, RNA recognition motif 3 / SHARP, RNA recognition motif 4 / : / : / : / Msx2-interacting protein, RAM7 domain / Msx2-interacting protein, MID domain / Msx2-interacting protein, nuclear receptor-interacting domain / Spen paralogue/orthologue C-terminal, metazoa / SPOC domain profile. / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / SPOC-like, C-terminal domain superfamily / SANT domain profile. / SANT domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Homeobox-like domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Msx2-interacting protein / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsMikami, S. / Kanaba, T. / Mishima, M.
CitationJournal: Structure / Year: 2014
Title: Structural insights into the recruitment of SMRT by the corepressor SHARP under phosphorylative regulation.
Authors: Mikami, S. / Kanaba, T. / Takizawa, N. / Kobayashi, A. / Maesaki, R. / Fujiwara, T. / Ito, Y. / Mishima, M.
History
DepositionApr 22, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_spectrometer / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Msx2-interacting protein
B: peptide from Silencing mediator of retinoic acid and thyroid hormone receptor


Theoretical massNumber of molelcules
Total (without water)19,5742
Polymers19,5742
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Msx2-interacting protein / SMART/HDAC1-associated repressor protein / SPEN homolog


Mass: 18471.402 Da / Num. of mol.: 1 / Fragment: SPOC domain, residues 3496-3664
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q96T58
#2: Protein/peptide peptide from Silencing mediator of retinoic acid and thyroid hormone receptor


Mass: 1102.880 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y618

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CO
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D C(CO)NH
1713D H(CCO)NH
1814D HC(CO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY-HSQC
11113D 1H-13C NOESY-HSQC
11212D 1H-13C HSQC
11313D CBCA(CO)NH
11413D HN(CA)CB
11513D C(CO)NH
11613D H(CCO)NH
11713D (H)CCH-TOCSY
11812D 15N filtered 1H NOESY
11913D HNHB
12013D HN(CO)HB
12113D 15N edited NOESY-HSQC
12213D 13C edited NOESY-HSQC

-
Sample preparation

DetailsSolvent system: 93% H2O/7% D2O
Sample conditionsIonic strength: 0 / pH: 7.5 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

-
Processing

NMR softwareName: CNS / Classification: refinement
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 / 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