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- PDB-1s4z: HP1 chromo shadow domain in complex with PXVXL motif of CAF-1 -

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Basic information

Entry
Database: PDB / ID: 1s4z
TitleHP1 chromo shadow domain in complex with PXVXL motif of CAF-1
Components
  • Chromatin assembly factor 1 subunit A
  • Chromobox protein homolog 1
KeywordsGENE REGULATION
Function / homology
Function and homology information


chromatin organization => GO:0006325 / CAF-1 complex / chromocenter / chromatin => GO:0000785 / histone methyltransferase binding / chromo shadow domain binding / DNA replication-dependent chromatin assembly / male pronucleus / female pronucleus / site of DNA damage ...chromatin organization => GO:0006325 / CAF-1 complex / chromocenter / chromatin => GO:0000785 / histone methyltransferase binding / chromo shadow domain binding / DNA replication-dependent chromatin assembly / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / pericentric heterochromatin / methylated histone binding / spindle / nucleosome assembly / chromatin organization / DNA replication / chromosome, telomeric region / nuclear body / cell cycle / DNA repair / 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 / identical protein binding / nucleus
Similarity search - Function
Chromatin assembly factor 1 subunit p150, N-terminal / Chromatin assembly factor 1 subunit p150, C-terminal / CAF1 complex subunit p150, region binding to CAF1-p60 at C-term / CAF1 complex subunit p150, region binding to PCNA / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup ...Chromatin assembly factor 1 subunit p150, N-terminal / Chromatin assembly factor 1 subunit p150, C-terminal / CAF1 complex subunit p150, region binding to CAF1-p60 at C-term / CAF1 complex subunit p150, region binding to PCNA / Chromatin assembly factor 1 subunit A / Chromatin assembly factor 1 subunit A / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromobox protein homolog 1 / Chromobox protein homolog 1 / Chromatin assembly factor 1 subunit A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / CNS, ARIA1.1
AuthorsThiru, A. / Nietlispach, D. / Mott, H.R. / Okuwaki, M. / Lyon, D. / Nielsen, P.R. / Hirshberg, M. / Verreault, A. / Murzina, N.V. / Laue, E.D.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin.
Authors: Thiru, A. / Nietlispach, D. / Mott, H.R. / Okuwaki, M. / Lyon, D. / Nielsen, P.R. / Hirshberg, M. / Verreault, A. / Murzina, N.V. / Laue, E.D.
History
DepositionJan 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 1
B: Chromobox protein homolog 1
C: Chromatin assembly factor 1 subunit A


Theoretical massNumber of molelcules
Total (without water)20,3653
Polymers20,3653
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #14closest to the average

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Components

#1: Protein Chromobox protein homolog 1 / Heterochromatin protein 1 homolog beta / HP1 beta / Modifier 1 protein / M31 / Heterochromatin protein p25


Mass: 8625.710 Da / Num. of mol.: 2 / Fragment: chromo shadow domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CBX1, CBX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P23197, UniProt: P83917*PLUS
#2: Protein/peptide Chromatin assembly factor 1 subunit A / CAF-1 subunit A / Chromatin assembly factor I p150 subunit / CAF-I 150 kDa subunit / CAF-Ip150


Mass: 3113.664 Da / Num. of mol.: 1 / Fragment: Chromatin Assembly Factor 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CHAF1A, CAIP150 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9QWF0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
2323D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
115N-labelled and 13C,15N labelled material complexed with unlabelled peptideH2O
215N labelled peptide complexed with unlabelled proteinH2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1150mM 7.5 1 atm298 K
2150mM 7.5 1 atm298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: CNS, ARIA1.1 / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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