[English] 日本語
Yorodumi
- PDB-1guw: STRUCTURE OF THE CHROMODOMAIN FROM MOUSE HP1beta IN COMPLEX WITH ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1guw
TitleSTRUCTURE OF THE CHROMODOMAIN FROM MOUSE HP1beta IN COMPLEX WITH THE LYSINE 9-METHYL HISTONE H3 N-TERMINAL PEPTIDE, NMR, 25 STRUCTURES
Components
  • CHROMOBOX PROTEIN HOMOLOG 1
  • HISTONE H3.1
KeywordsCHROMATIN-BINDING / LYSINE METHYLATION / HETEROCHROMATIN / HISTONE MODIFICATION
Function / homology
Function and homology information


chromatin organization => GO:0006325 / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis ...chromatin organization => GO:0006325 / Chromatin modifying enzymes / Interleukin-7 signaling / HDMs demethylate histones / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / HDACs deacetylate histones / PRC2 methylates histones and DNA / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / chromocenter / Factors involved in megakaryocyte development and platelet production / histone methyltransferase binding / Estrogen-dependent gene expression / DNA replication-dependent chromatin assembly / male pronucleus / female pronucleus / nuclear chromosome / site of DNA damage / chromosome, centromeric region / pericentric heterochromatin / Chromatin modifying enzymes / : / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear body / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / Chromobox protein homolog 1 / Histone H3.1 / Chromobox protein homolog 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsNielsen, P.R. / Nietlispach, D. / Mott, H.R. / Callaghan, J.M. / Bannister, A. / Kouzarides, T. / Murzin, A.G. / Murzina, N.V. / Laue, E.D.
Citation
Journal: Nature / Year: 2002
Title: Structure of the Hp1 Chromodomain Bound to Histone H3 Methylated at Lysine 9
Authors: Nielsen, P.R. / Nietlispach, D. / Mott, H.R. / Callaghan, J.M. / Bannister, A. / Kouzarides, T. / Murzin, A.G. / Murzina, N.V. / Laue, E.D.
#1: Journal: Embo J. / Year: 1997
Title: Structure of the Chromatin Binding (Chromo) Domain from Mouse Modifier Protein 1
Authors: Ball, L.J. / Murzina, N.V. / Broadhurst, R.W. / Raine, A.R. / Archer, S.J. / Stott, F.J. / Murzin, A.G. / Singh, P.B. / Domaille, P.J. / Laue, E.D.
History
DepositionFeb 1, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHROMOBOX PROTEIN HOMOLOG 1
B: HISTONE H3.1


Theoretical massNumber of molelcules
Total (without water)10,5262
Polymers10,5262
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)25 / 100LOWEST ENERGY OF 75 CONVERGED STRUCTURES
RepresentativeModel #1

-
Components

#1: Protein CHROMOBOX PROTEIN HOMOLOG 1 / HETEROCHROMATIN PROTEIN 1 HOMOLOG BETA / HP1 BETA / MODIFIER 1 PROTEIN / M31


Mass: 8694.559 Da / Num. of mol.: 1 / Fragment: CHROMODOMAIN, RESIDUES 8 - 80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23197, UniProt: P83917*PLUS
#2: Protein/peptide HISTONE H3.1 / HISTONE H3 / NUCLEAR PROTEIN / CHROMOSOMAL PROTEIN / DNA-BINDING / NUCLEOSOME CORE / MULTIGENE ...HISTONE H3 / NUCLEAR PROTEIN / CHROMOSOMAL PROTEIN / DNA-BINDING / NUCLEOSOME CORE / MULTIGENE FAMILY / METHYLATION


Mass: 1831.108 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TAIL, RESIDUES 1-18 / Source method: obtained synthetically
Details: BOTH CHEMICALLY SYTHESIZED PEPTIDE AND PEPTIDE OBTAINED FROM EXPRESSION IN BACTERIA WERE USED.
Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P16106, UniProt: P68433*PLUS
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D
1213D 1H
13115N
14113C
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE 2D AND 3D NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN. FOR PROTEIN ASSIGMENTS THE SAMPLE CONTAINED AN EXCESS OF 1.2 FOLD OF UNLABELLED ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE 2D AND 3D NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN. FOR PROTEIN ASSIGMENTS THE SAMPLE CONTAINED AN EXCESS OF 1.2 FOLD OF UNLABELLED PEPTIDE. THE PEPTIDE WAS ASSIGNED USING 13C, 15N REJECTED NOESY AND TOCSY EXPERIMENTS ON A SAMPLE OF EXCESS 13C, 15N LABELLED PROTEIN TO UNLABELLED PEPTIDE. THE METHYL GROUP RESONANCES OF LYSINE 4 AND 9 OF THE PEPTIDE WERE CONFIRMED WITH THE HELP OF A 13C METHYL-SELECTIVELY LABELLED SAMPLE MIXED WITH UNLABELLED PROTEIN. INTERMOLECULAR CONTACTS WERE OBTAINED FROM A 13C/15N X-FILTERED NOESY SPECTRUM AND A 3D J(CH,NH)- SEPARATED NOESY SPECTRUM

-
Sample preparation

DetailsContents: 150 mM NACL, 20 mM PHOSPHATE BUFFER, 10% D2O
Sample conditionspH: 5.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameDeveloperClassification
ARIAJ.P.LINGE,S.I.O'DONOGHUE,M.NILGESrefinement
Azarastructure solution
ANSIGstructure solution
ARIAstructure solution
CNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY OF 75 CONVERGED STRUCTURES
Conformers calculated total number: 100 / Conformers submitted total number: 25

+
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