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- PDB-1pdq: Polycomb chromodomain complexed with the histone H3 tail containi... -

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Basic information

Entry
Database: PDB / ID: 1pdq
TitlePolycomb chromodomain complexed with the histone H3 tail containing trimethyllysine 27.
Components
  • Histone H3.3H3F3A
  • Polycomb proteinPolycomb-group proteins
KeywordsSTRUCTURAL PROTEIN / methyllysine / chromodomain / histone H3 / polycomb / lysine methylation / trimethyllysine / cation-pi / chromo
Function / homology
Function and homology information


negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / ventral cord development ...negative regulation of response to gamma radiation / specification of segmental identity, abdomen / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of DNA damage response and repair proteins / SUMOylation of RNA binding proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / syncytial blastoderm mitotic cell cycle / polytene chromosome band / ventral cord development / PRC1 complex / polytene chromosome / nucleosomal DNA binding / anterior/posterior axis specification / neuron remodeling / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / heterochromatin formation / methylated histone binding / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / neurogenesis / DNA methylation / Condensation of Prophase Chromosomes / 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 / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / wound healing / 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 / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / sequence-specific DNA binding / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / chromatin / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus
Similarity search - Function
CBX family C-terminal motif / CBX family C-terminal motif / 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 ...CBX family C-terminal motif / CBX family C-terminal motif / 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 H3.3 / Polycomb group protein Pc / Histone H3.3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsFischle, W. / Wang, Y. / Jacobs, S.A. / Kim, Y. / Allis, C.D. / Khorasanizadeh, S.
CitationJournal: Genes Dev. / Year: 2003
Title: Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains
Authors: Fischle, W. / Wang, Y. / Jacobs, S.A. / Kim, Y. / Allis, C.D. / Khorasanizadeh, S.
History
DepositionMay 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein
B: Histone H3.3


Theoretical massNumber of molelcules
Total (without water)10,7822
Polymers10,7822
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-6 kcal/mol
Surface area4230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.120, 75.810, 80.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

21A-241-

HOH

31A-248-

HOH

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Components

#1: Protein Polycomb protein / Polycomb-group proteins


Mass: 8853.055 Da / Num. of mol.: 1 / Fragment: residues 15-77
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PC OR CG7618 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P26017
#2: Protein/peptide Histone H3.3 / H3F3A / H3.A / H3.B / H3.3Q


Mass: 1929.290 Da / Num. of mol.: 1 / Fragment: residues 15-32 / Mutation: K27(M3L) / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P06351, UniProt: P84243*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, 0.2 M Lithium sulfate, 30 % PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 10 or 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
250 mM1dropNaCl
35 mg/mlprotein1drop
40.1 MTris-HCl1reservoirpH8.5
50.2 M1reservoirLi2SO4
630 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2003
RadiationMonochromator: double crystal SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 9494 / Num. obs: 9494 / % possible obs: 93.7 % / Observed criterion σ(F): 2.95 / Observed criterion σ(I): 2.95 / Redundancy: 4.1 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.033 / Net I/σ(I): 32.6
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 2.95 / Num. unique all: 1190 / Rsym value: 0.212 / % possible all: 74.2
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 74.2 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.212

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1KNA

1kna


Resolution: 1.76→27.59 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 985 10.4 %RANDOM
Rwork0.223 ---
all0.223 9494 --
obs0.223 9494 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.0875 Å2 / ksol: 0.405418 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å20 Å20 Å2
2---0.59 Å20 Å2
3---3.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.76→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms516 0 0 194 710
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.57
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.482.5
LS refinement shellResolution: 1.76→1.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 134 10.1 %
Rwork0.274 1190 -
obs--79.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TEST2.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2523 / Rfactor Rwork: 0.2233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00574
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.57

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