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- PDB-1guw: STRUCTURE OF THE CHROMODOMAIN FROM MOUSE HP1beta IN COMPLEX WITH ... -

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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 / Estrogen-dependent gene expression / histone methyltransferase binding / 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 / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / 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 / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / 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 domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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

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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

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NMR measurement

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

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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

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