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- PDB-1kna: Chromo domain of HP1 complexed with histone H3 tail containing di... -

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Basic information

Entry
Database: PDB / ID: 1kna
TitleChromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
Components
  • HETEROCHROMATIN PROTEIN 1
  • METHYLATED Histone H3
KeywordsSTRUCTURAL PROTEIN / chromo / HP1 / histone / dimethyllysine / methyllysine / H3
Function / homology
Function and homology information


protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / siRNA-mediated heterochromatin formation / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / SIRT1 negatively regulates rRNA expression ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / siRNA-mediated heterochromatin formation / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / Factors involved in megakaryocyte development and platelet production / RCAF complex / SIRT1 negatively regulates rRNA expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / satellite DNA binding / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Regulation of endogenous retroelements by KRAB-ZFP proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Senescence-Associated Secretory Phenotype (SASP) / Transcriptional regulation by small RNAs / Estrogen-dependent gene expression / HATs acetylate histones / Assembly of the ORC complex at the origin of replication / Oxidative Stress Induced Senescence / transposable element silencing by piRNA-mediated heterochromatin formation / polytene chromosome / chromocenter / rDNA binding / condensed chromosome, centromeric region / pericentric heterochromatin formation / regulation of protein localization to chromatin / RNA polymerase binding / nucleosomal DNA binding / RNA polymerase II C-terminal domain binding / chromosome, centromeric region / chromosome organization / heterochromatin / pericentric heterochromatin / : / condensed chromosome / Hsp70 protein binding / telomere maintenance / euchromatin / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / chromosome / protein-macromolecule adaptor activity / histone binding / chromosome, telomeric region / protein heterodimerization activity / negative regulation of DNA-templated transcription / mRNA binding / chromatin binding / regulation of DNA-templated transcription / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / 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. / 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 / Heterochromatin protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJacobs, S.A. / Khorasanizadeh, S.
CitationJournal: Science / Year: 2002
Title: Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail.
Authors: Jacobs, S.A. / Khorasanizadeh, S.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HETEROCHROMATIN PROTEIN 1
P: METHYLATED Histone H3


Theoretical massNumber of molelcules
Total (without water)10,3422
Polymers10,3422
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-4 kcal/mol
Surface area4040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.792, 76.883, 75.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-146-

HOH

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Components

#1: Protein HETEROCHROMATIN PROTEIN 1 / HP1 / NONHISTONE CHROMOSOMAL PROTEIN C1A9 ANTIGEN


Mass: 8586.468 Da / Num. of mol.: 1 / Fragment: Residues 23-76 / Mutation: K38M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3)pLysS / References: UniProt: P05205
#2: Protein/peptide METHYLATED Histone H3


Mass: 1756.017 Da / Num. of mol.: 1 / Fragment: Residues 1-16 / Mutation: P16Y / Source method: obtained synthetically
Details: Synthetic peptide Corresponding to residues 1-16 of Histone H3. K9 dimethylated. P16Y mutation.
References: UniProt: P02299
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283.0K
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 6.1 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-IDDetails
1ammonium sulfate1reservoir
2MES1reservoirpH6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 6032 / Num. obs: 6032 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.079 / Net I/σ(I): 61.6
Reflection shellResolution: 2.1→2.23 Å / Mean I/σ(I) obs: 10.5 / Num. unique all: 842 / Rsym value: 0.279 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.279

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.63 Å / Rfactor Rfree error: 0.026 / Data cutoff high rms absF: 117307.12 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 654 10.9 %RANDOM
Rwork0.228 ---
all-6008 --
obs-5354 99.8 %-
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.6 Å2-3.48 Å2-2.11 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms499 0 0 86 585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.59
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 116 12.1 %
Rwork0.245 842 -
obs--99.3 %
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.59

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