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- PDB-3ij0: Crystal structure of Eed in complex with a trimethylated histone ... -

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Basic information

Entry
Database: PDB / ID: 3ij0
TitleCrystal structure of Eed in complex with a trimethylated histone H3K9 peptide
Components
  • Histone H3K9 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 / MOLECULAR REPLACEMENT / Resolution: 2.45 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 1.2Oct 13, 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 1.3Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Polycomb protein EED
B: Histone H3K9 peptide


Theoretical massNumber of molelcules
Total (without water)43,3472
Polymers43,3472
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-5.7 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.583, 85.087, 91.266
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: 42139.922 Da / Num. of mol.: 1 / Fragment: Eed residues 77-441 / Mutation: M370T
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 H3K9 peptide


Mass: 1207.424 Da / Num. of mol.: 1 / Fragment: Histone H3K9 peptide residues 4-14 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 16201 / Num. obs: 16201 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 9.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.352 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet Eed structure

Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.888 / SU B: 7.493 / SU ML: 0.172 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.489 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24412 834 5.1 %RANDOM
Rwork0.18111 ---
all0.18428 15472 --
obs0.18428 15472 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---1.16 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 230 3174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213013
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.9294083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6985362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97223.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08115513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7821520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022294
X-RAY DIFFRACTIONr_nbd_refined0.1870.21317
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22023
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.213
X-RAY DIFFRACTIONr_mcbond_it0.5211.51863
X-RAY DIFFRACTIONr_mcangle_it0.91622928
X-RAY DIFFRACTIONr_scbond_it1.32331332
X-RAY DIFFRACTIONr_scangle_it2.2044.51155
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 71 -
Rwork0.216 1142 -
obs--98.22 %

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