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- PDB-3ij1: Crystal structure of Eed in complex with a trimethylated histone ... -

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Basic information

Entry
Database: PDB / ID: 3ij1
TitleCrystal structure of Eed in complex with a trimethylated histone H4K20 peptide
Components
  • Histone H4K20 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 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / nucleosome binding / enzyme activator activity / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / nucleosome binding / enzyme activator activity / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / HATs acetylate histones / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein heterodimerization activity / Amyloid fiber formation / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone-fold / 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 / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 H4K20 peptide


Theoretical massNumber of molelcules
Total (without water)43,5812
Polymers43,5812
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4.2 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.550, 85.321, 91.229
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
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 H4K20 peptide


Mass: 1440.740 Da / Num. of mol.: 1 / Fragment: Histone H4K20 peptide residues 15-25 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: P62805*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
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: 2.1→50 Å / Num. all: 25569 / Num. obs: 25569 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.321 / % possible all: 99.1

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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 model

Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.607 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20356 1333 5 %RANDOM
Rwork0.16631 ---
all0.16819 25288 --
obs0.16819 25288 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.463 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---0.67 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 0 400 3381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213056
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9294140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40823.618152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53215526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5371522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022330
X-RAY DIFFRACTIONr_nbd_refined0.1840.21321
X-RAY DIFFRACTIONr_nbtor_refined0.30.22060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2399
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.227
X-RAY DIFFRACTIONr_mcbond_it0.5981.51893
X-RAY DIFFRACTIONr_mcangle_it0.99122957
X-RAY DIFFRACTIONr_scbond_it1.41931354
X-RAY DIFFRACTIONr_scangle_it2.3284.51183
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 93 -
Rwork0.168 1854 -
obs--98.83 %

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