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- PDB-1q3l: Chromodomain Of HP1 Complexed With Histone H3 Tail Containing mon... -

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Basic information

Entry
Database: PDB / ID: 1q3l
TitleChromodomain Of HP1 Complexed With Histone H3 Tail Containing monomethyllysine 9.
Components
  • Heterochromatin protein 1
  • Histone H3
KeywordsSTRUCTURAL PROTEIN / chromodomain / HP1 / chromatin / methyllysine / monomethyllysine / histone / H3
Function / homology
Function and homology information


protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / chromatin organization => GO:0006325 / satellite DNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / pericentric heterochromatin formation / chromocenter / polytene chromosome ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / chromatin organization => GO:0006325 / satellite DNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / pericentric heterochromatin formation / chromocenter / polytene chromosome / rDNA binding / DNA replication-dependent chromatin assembly / condensed chromosome, centromeric region / regulation of protein localization to chromatin / RNA polymerase binding / nuclear chromosome / RNA polymerase II C-terminal domain binding / chromosome, centromeric region / chromosome organization / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / condensed chromosome / Hsp70 protein binding / methylated histone binding / telomere organization / telomere maintenance / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates 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 / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / protein-macromolecule adaptor activity / mitotic cell cycle / gene expression / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / mRNA binding / negative regulation of DNA-templated transcription / chromatin binding / protein-containing complex binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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/chromo shadow domain ...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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / 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
Heterochromatin protein 1 / Histone H3.1 / Histone H3.1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsJacobs, S.A. / Khorasanizadeh, S.
CitationJournal: To be Published
Title: Chromodomain Of HP1 Complexed With Histone H3 Tail Containing monomethyllysine 9
Authors: Jacobs, S.A. / Khorasanizadeh, S.
History
DepositionJul 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Histone H3


Theoretical massNumber of molelcules
Total (without water)10,3282
Polymers10,3282
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-4 kcal/mol
Surface area4120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.809, 76.828, 75.625
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-82-

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: sequence database residues 17-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: SU(VAR)205 OR HP1 OR CG8409 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05205
#2: Protein/peptide Histone H3 /


Mass: 1741.990 Da / Num. of mol.: 1 / Fragment: tail residues 1-16 / Source method: obtained synthetically
Details: The peptide is chemically synthesized. The sequence is naturally found in Homo sapiens (human).
References: UniProt: P16106, UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: Ammonium Sulfate, MES, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9208 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9208 Å / Relative weight: 1
ReflectionResolution: 1.64→38.35 Å / Num. all: 10752 / Num. obs: 10752 / % possible obs: 0.9057 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.37 % / Rsym value: 0.051 / Net I/σ(I): 52.9
Reflection shellResolution: 1.64→1.7 Å / Mean I/σ(I) obs: 20.5 / Num. unique all: 1211 / Rsym value: 0.143 / % possible all: 0.988

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNA

1kna


Resolution: 1.64→38.35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.924 / SU B: 1.174 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24091 537 4.8 %RANDOM
Rwork0.22218 ---
all0.22315 10752 --
obs0.22315 10752 90.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.511 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2---1.05 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.64→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 0 95 593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021509
X-RAY DIFFRACTIONr_bond_other_d0.0020.02442
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.958683
X-RAY DIFFRACTIONr_angle_other_deg1.24131033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.727556
X-RAY DIFFRACTIONr_chiral_restr0.4310.268
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02567
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02108
X-RAY DIFFRACTIONr_nbd_refined0.2260.2104
X-RAY DIFFRACTIONr_nbd_other0.260.2540
X-RAY DIFFRACTIONr_nbtor_other0.1130.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.211
X-RAY DIFFRACTIONr_mcbond_it1.2061.5290
X-RAY DIFFRACTIONr_mcangle_it2.1242466
X-RAY DIFFRACTIONr_scbond_it3.0193219
X-RAY DIFFRACTIONr_scangle_it4.8714.5217
LS refinement shellResolution: 1.64→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 40 -
Rwork0.13 874 -
obs-1211 0.988 %

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