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- PDB-3iiw: Crystal structure of Eed in complex with a trimethylated histone ... -

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Basic information

Entry
Database: PDB / ID: 3iiw
TitleCrystal structure of Eed in complex with a trimethylated histone H3K27 peptide
Components
  • Histone H3 peptide
  • Polycomb protein EED
KeywordsGENE REGULATION / WD40 domain / Alternative initiation / Alternative splicing / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / WD repeat
Function / homology
Function and homology information


ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / nucleosome binding / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / nucleosome binding / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / chromosome / Oxidative Stress Induced Senescence / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJustin, N. / Sharpe, M.L. / Martin, S. / Taylor, W.R. / De Marco, V. / Gamblin, S.J.
CitationJournal: Nature / Year: 2009
Title: Role of the polycomb protein EED in the propagation of repressive histone marks.
Authors: Margueron, R. / Justin, N. / Ohno, K. / Sharpe, M.L. / Son, J. / Drury, W.J. / Voigt, P. / Martin, S.R. / Taylor, W.R. / De Marco, V. / Pirrotta, V. / Reinberg, D. / Gamblin, S.J.
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polycomb protein EED
B: Histone H3 peptide


Theoretical massNumber of molelcules
Total (without water)43,3162
Polymers43,3162
Non-polymers00
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-5.7 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.745, 85.118, 91.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE BIOLOGICAL UNIT CONTAINS A MONOMERIC COMPLEX COMPOSED FROM PROTEIN CHAIN A AND PEPTIDE CHAIN B, THEREFORE IT IS NOT A DIMER AS THE TEXT IN REMARK 350 STATES

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Components

#1: Protein Polycomb protein EED / hEED / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 42170.016 Da / Num. of mol.: 1 / Fragment: Eed residues 77-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O75530
#2: Protein/peptide Histone H3 peptide


Mass: 1146.360 Da / Num. of mol.: 1 / Fragment: Histone H3 peptide residues 22-31 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4.0 M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
Details: Kirkpatrick-Baez bimorph mirror pair for horizontal and vertical focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 40269 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 20.37 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.077 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.303 / % possible all: 85.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet Eed structure

Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.165 / SU ML: 0.067 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19315 2084 5 %RANDOM
Rwork0.15711 ---
all0.15896 39383 --
obs0.15896 39383 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 0 404 3347
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213016
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.934084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1345362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52923.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75515518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.091520
X-RAY DIFFRACTIONr_chiral_restr0.1390.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212294
X-RAY DIFFRACTIONr_mcbond_it1.7161.51811
X-RAY DIFFRACTIONr_mcangle_it2.83722926
X-RAY DIFFRACTIONr_scbond_it4.22531205
X-RAY DIFFRACTIONr_scangle_it6.584.51158
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 128 -
Rwork0.24 2406 -
obs--82.84 %

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