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- PDB-2rsn: Solution structure of the chromodomain of Chp1 in complex with H3... -

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Basic information

Entry
Database: PDB / ID: 2rsn
TitleSolution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide
Components
  • Chromo domain-containing protein 1
  • peptide from Histone H3
KeywordsNUCLEAR PROTEIN / chromodomain / protein-peptide complex / RNA-mediated gene silencing / Chromosomal protein / Methylation
Function / homology
Function and homology information


RITS complex / siRNA-mediated pericentric heterochromatin formation / mating-type region heterochromatin / heterochromatin island / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / regulatory ncRNA-mediated heterochromatin formation / chromosome, subtelomeric region / replication fork protection complex ...RITS complex / siRNA-mediated pericentric heterochromatin formation / mating-type region heterochromatin / heterochromatin island / sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / regulatory ncRNA-mediated heterochromatin formation / chromosome, subtelomeric region / replication fork protection complex / spindle pole body / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / subtelomeric heterochromatin formation / pericentric heterochromatin / CENP-A containing nucleosome / methylated histone binding / histone reader activity / chromosome segregation / structural constituent of chromatin / nucleosome / chromatin organization / histone binding / single-stranded RNA binding / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
: / Chromo domain-containing protein 1-like, PIN domain / 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 domain-containing protein 1-like, PIN domain / 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. / RNA-binding domain superfamily / 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 / Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsShimojo, H. / Nishimura, Y.
CitationJournal: Mol.Cell / Year: 2012
Title: Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing
Authors: Ishida, M. / Shimojo, H. / Hayashi, A. / Kawaguchi, R. / Ohtani, Y. / Uegaki, K. / Nishimura, Y. / Nakayama, J.
History
DepositionApr 18, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromo domain-containing protein 1
B: peptide from Histone H3


Theoretical massNumber of molelcules
Total (without water)10,9352
Polymers10,9352
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromo domain-containing protein 1


Mass: 8909.912 Da / Num. of mol.: 1 / Fragment: Chromo domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: chp1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10103
#2: Protein/peptide peptide from Histone H3 /


Mass: 2025.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Schizosaccharomyces pombe (fission yeast) / References: UniProt: P61830*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
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D HN(CA)CO
1913D CBCA(CO)NH
11013D HBHA(CO)NH
11113D (H)CCH-COSY
11213D (H)CCH-TOCSY
11313D 1H-15N NOESY
11413D 1H-13C NOESY aliphatic
11513D 1H-13C NOESY aromatic
11613D 13C/15N filtered NOESY
11712D 13C/15N fllterd NOESY
11812D 13C/15N filterd TOCSY

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Sample preparation

DetailsContents: 0.3-0.5mM [U-99% 13C; U-99% 15N] Chp1_chromodomain-1, 0.3-0.5mM Histone_H3K9me3-2, 20mM potassium phosphate-3, 10mM sodium chloride-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMChp1_chromodomain-1[U-99% 13C; U-99% 15N]0.3-0.51
mMHistone_H3K9me3-20.3-0.51
20 mMpotassium phosphate-31
10 mMsodium chloride-41
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 AvanceBrukerAvance8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
OliviaYokochi, Sekiguchi and Inagakichemical shift assignment
OliviaYokochi, Sekiguchi and Inagakidata analysis
OliviaYokochi, Sekiguchi and Inagakipeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CYANArefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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