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- PDB-2rvn: Solution structure of the chromodomain of HP1a with the phosphory... -

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Basic information

Entry
Database: PDB / ID: 2rvn
TitleSolution structure of the chromodomain of HP1a with the phosphorylated N-terminal tail complexed with H3K9me3 peptide
Components
  • 18-mer peptide of Histone H3
  • Chromobox protein homolog 5
KeywordsTRANSCRIPTION/PEPTIDE / chromodomain / hp1alpha / TRANSCRIPTION-PEPTIDE complex
Function / homology
Function and homology information


Inhibition of DNA recombination at telomere / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / chromocenter / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / Factors involved in megakaryocyte development and platelet production ...Inhibition of DNA recombination at telomere / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / chromocenter / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / Factors involved in megakaryocyte development and platelet production / Estrogen-dependent gene expression / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / histone methyltransferase complex / oogenesis / nucleus organization / site of DNA damage / histone deacetylase complex / chromosome, centromeric region / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / ribonucleoprotein complex binding / pericentric heterochromatin / heterochromatin / nucleosomal DNA binding / transcription repressor complex / embryo implantation / methylated histone binding / multicellular organism growth / PML body / heterochromatin formation / kinetochore / histone deacetylase binding / osteoblast differentiation / male gonad development / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / protein-macromolecule adaptor activity / positive regulation of cell growth / spermatogenesis / DNA-binding transcription factor binding / cell population proliferation / chromosome, telomeric region / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
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. / 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
Similarity search - Domain/homology
Histone H3.3 / Chromobox protein homolog 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsKawaguchi, A. / Nishimura, Y.
CitationJournal: Sci Rep / Year: 2016
Title: Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail
Authors: Shimojo, H. / Kawaguchi, A. / Oda, T. / Hashiguchi, N. / Omori, S. / Moritsugu, K. / Kidera, A. / Hiragami-Hamada, K. / Nakayama, J. / Sato, M. / Nishimura, Y.
History
DepositionDec 18, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 5
B: 18-mer peptide of Histone H3


Theoretical massNumber of molelcules
Total (without water)12,1942
Polymers12,1942
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 / 600structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromobox protein homolog 5 / Heterochromatin protein 1 homolog alpha / HP1 alpha


Mass: 10169.046 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: For phosphorylation of Ser the expression with pRSFduet (CK2)
Gene: Cbx5, Hp1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q61686
#2: Protein/peptide 18-mer peptide of Histone H3


Mass: 2025.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P84244*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC aliphatic
1322D 1H-13C HSQC aromatic
1412D 1H-1H TOCSY
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HN(CO)CA
11113D HBHA(CO)NH
11223D (H)CCH-TOCSY
11313D 1H-15N NOESY
11423D 1H-13C NOESY aliphatic
11523D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM [U-99% 13C; U-99% 15N] potassium phosphate-1, 10 mM [U-99% 13C; U-99% 15N] sodium chloride-2, 5 mM [U-99% 13C; U-99% 15N] DTT-3, 90% H2O/10% D2O90% H2O/10% D2O
220 mM [U-99% 13C; U-99% 15N] potassium phosphate-4, 10 mM [U-99% 13C; U-99% 15N] sodium chloride-5, 5 mM [U-99% 13C; U-99% 15N] DTT-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMpotassium phosphate-1[U-99% 13C; U-99% 15N]1
10 mMsodium chloride-2[U-99% 13C; U-99% 15N]1
5 mMDTT-3[U-99% 13C; U-99% 15N]1
20 mMpotassium phosphate-4[U-99% 13C; U-99% 15N]2
10 mMsodium chloride-5[U-99% 13C; U-99% 15N]2
5 mMDTT-6[U-99% 13C; U-99% 15N]2
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceBrukerAvance7002
Bruker AvanceBrukerAvance8003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
OliviaYokochi, M., Sekiguchi, S. and Inagaki, F.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 600 / Conformers submitted total number: 20 / Representative conformer: 1

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