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- PDB-6at0: Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at posit... -

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Basic information

Entry
Database: PDB / ID: 6at0
TitleChromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone H3 peptide containing trimethyl lysine
Components
  • Heterochromatin protein 1
  • trimethyl lysine histone H3 tail peptide
KeywordsTRANSCRIPTION / histone reader
Function / homology
Function and homology information


protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...protein localization to euchromatin / positive regulation of FACT complex assembly / polytene chromosome chromocenter / polytene chromosome puff / Interleukin-7 signaling / Chromatin modifying enzymes / RCAF complex / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / satellite DNA binding / positive regulation of DNA methylation-dependent heterochromatin formation / pericentric heterochromatin formation / chromocenter / polytene chromosome / rDNA binding / condensed chromosome, centromeric region / 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 / heterochromatin formation / condensed chromosome / Hsp70 protein binding / methylated histone binding / telomere maintenance / euchromatin / nucleosome assembly / structural constituent of chromatin / nucleosome / protein-macromolecule adaptor activity / mitotic cell cycle / chromosome / chromatin organization / histone binding / chromosome, telomeric region / protein heterodimerization activity / negative regulation of gene expression / mRNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / 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 / 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/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
Histone H3 / Heterochromatin protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.285 Å
AuthorsBrustad, E.M. / Baril, S.A. / Waters, M.L.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis.
Authors: Baril, S.A. / Koenig, A.L. / Krone, M.W. / Albanese, K.I. / He, C.Q. / Lee, G.Y. / Houk, K.N. / Waters, M.L. / Brustad, E.M.
History
DepositionAug 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterochromatin protein 1
P: trimethyl lysine histone H3 tail peptide


Theoretical massNumber of molelcules
Total (without water)9,3492
Polymers9,3492
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-5 kcal/mol
Surface area4170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.417, 76.857, 76.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-135-

HOH

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Components

#1: Protein Heterochromatin protein 1 / / HP1 / Non-histone chromosomal protein C1A9 antigen


Mass: 8615.466 Da / Num. of mol.: 1 / Fragment: Chromo 1 domain, residues 17-76 / Mutation: K38M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su(var)205, HP1, CG8409 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P05205
#2: Protein/peptide trimethyl lysine histone H3 tail peptide


Mass: 733.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P02299*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 0.1M MES, 3.0M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.285→11.224 Å / Num. obs: 25429 / % possible obs: 96.9 % / Redundancy: 5.36 % / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNE

1kne


Resolution: 1.285→11.224 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 39.01
RfactorNum. reflection% reflection
Rfree0.2597 1291 5.08 %
Rwork0.241 --
obs0.2418 25429 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.3 Å2 / Biso mean: 28.7653 Å2 / Biso min: 13.75 Å2
Refinement stepCycle: final / Resolution: 1.285→11.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms511 0 0 40 551
Biso mean---37.51 -
Num. residues----59
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004551
X-RAY DIFFRACTIONf_angle_d0.751747
X-RAY DIFFRACTIONf_chiral_restr0.07474
X-RAY DIFFRACTIONf_plane_restr0.00498
X-RAY DIFFRACTIONf_dihedral_angle_d21.256217
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2845-1.33590.4871350.51292562269794
1.3359-1.39660.41771360.4592591272795
1.3966-1.470.39041430.40862609275296
1.47-1.56190.3111550.35662686284197
1.5619-1.68210.26681380.28392684282298
1.6821-1.85070.25261650.2272704286999
1.8507-2.1170.20321410.19872732287398
2.117-2.66130.23631490.2182752290198
2.6613-11.22420.24031290.20452818294796

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