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- PDB-6mha: dHP1 Chromodomain Y24W variant bound to histone H3 peptide contai... -

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Basic information

Entry
Database: PDB / ID: 6mha
TitledHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine
Components
  • Heterochromatin protein 1
  • histone H3 peptide containing trimethyllysine, H3K9me3
KeywordsPROTEIN BINDING / cation-pi epigenetics trimethyllysine chromodomain
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 / molecular replacement / Resolution: 1.497 Å
AuthorsBrustad, E.M. / Krone, M.W. / Albanese, K.I. / Waters, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM118499 United States
CitationJournal: Chem Sci / Year: 2020
Title: Thermodynamic consequences of Tyr to Trp mutations in the cation-pi-mediated binding of trimethyllysine by the HP1 chromodomain
Authors: Krone, M.W. / Albanese, K.I. / Guseman, A.J. / He, C.Q. / Lee, G.Y. / Houk, K.N. / Brustad, E.M. / Waters, M.L.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 21, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Heterochromatin protein 1
B: histone H3 peptide containing trimethyllysine, H3K9me3


Theoretical massNumber of molelcules
Total (without water)7,2932
Polymers7,2932
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area4110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.007, 76.695, 76.508
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-129-

HOH

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Components

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


Mass: 6559.268 Da / Num. of mol.: 1 / Mutation: Y24W, 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 histone H3 peptide containing trimethyllysine, H3K9me3


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.: 34 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 3.2 M Ammonium sulfate, 0.1 M MES / PH range: 5.5 - 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 19, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→38.347 Å / Num. obs: 30131 / % possible obs: 96.7 % / Redundancy: 3.533 % / Biso Wilson estimate: 22.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.045 / Χ2: 1.017 / Net I/σ(I): 19.79
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.592.4690.3122.9541010.9060.38281.6
1.59-1.73.6070.1866.3747110.9750.21999.4
1.7-1.833.5870.09312.0443890.9910.1199.3
1.83-2.013.7450.05718.940470.9960.06699.5
2.01-2.253.7960.0426.8336440.9980.04799.9
2.25-2.593.80.03431.8532380.9980.03999.9
2.59-3.173.8070.03135.8327360.9980.03699.9
3.17-4.483.7120.03538.821090.9960.04199.6
4.48-38.3473.5030.03938.0711560.9950.04698.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
KYLINdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNE

1kne


Resolution: 1.497→38.347 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2189 3009 10 %
Rwork0.1943 --
obs0.1968 30105 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.72 Å2 / Biso mean: 29.6315 Å2 / Biso min: 16.5 Å2
Refinement stepCycle: final / Resolution: 1.497→38.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms508 0 0 34 542
Biso mean---40.06 -
Num. residues----59
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006550
X-RAY DIFFRACTIONf_angle_d0.804748
X-RAY DIFFRACTIONf_chiral_restr0.08173
X-RAY DIFFRACTIONf_plane_restr0.00598
X-RAY DIFFRACTIONf_dihedral_angle_d25.863218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4973-1.52180.3314610.324655761842
1.5218-1.54810.34271500.2831326147696
1.5481-1.57620.25331400.23091279141998
1.5762-1.60650.23041500.22451334148499
1.6065-1.63930.1791480.195413191467100
1.6393-1.6750.23251550.19451361151699
1.675-1.7140.19411450.17941282142799
1.714-1.75680.22041440.18011317146199
1.7568-1.80430.22331500.178713481498100
1.8043-1.85740.26341470.18511318146599
1.8574-1.91740.22741450.1851331147699
1.9174-1.98590.18821470.185213401487100
1.9859-2.06540.20771470.195513151462100
2.0654-2.15940.20321520.190213261478100
2.1594-2.27320.23621470.191513561503100
2.2732-2.41560.1941470.20613231470100
2.4156-2.60210.25871500.217613381488100
2.6021-2.86390.20621450.209413211466100
2.8639-3.27810.20111500.207113301480100
3.2781-4.12930.22821440.164313481492100
4.1293-38.36010.21531450.19541327147299
Refinement TLS params.Method: refined / Origin x: -10.4939 Å / Origin y: -10.2958 Å / Origin z: 5.2353 Å
111213212223313233
T0.1902 Å20.0187 Å20.0074 Å2-0.1878 Å20.0072 Å2--0.1829 Å2
L1.7242 °2-0.0537 °20.1546 °2-1.8186 °20.1415 °2--0.9596 °2
S0.0093 Å °-0.0032 Å °-0.014 Å °-0.0047 Å °0.0032 Å °0.0242 Å °0.1302 Å °0.0052 Å °-0.0006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA22 - 74
2X-RAY DIFFRACTION1allB-3 - 2
3X-RAY DIFFRACTION1allS1 - 27
4X-RAY DIFFRACTION1allS28 - 34

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