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- PDB-4x3e: Crystal structure of EED in complex with a trimethylated Jarid2 p... -

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Basic information

Entry
Database: PDB / ID: 4x3e
TitleCrystal structure of EED in complex with a trimethylated Jarid2 peptide
Components
  • ALA-GLN-ARG-M3L-PHE-ALA-GLN-SER
  • Polycomb protein EED
KeywordsTRANSCRIPTION / Gene regulation / histone binding / WD40
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: 2.3 Å
AuthorsJustin, N. / Gamblin, S.J. / Margueron, R.
CitationJournal: Mol.Cell / Year: 2015
Title: Jarid2 Methylation via the PRC2 Complex Regulates H3K27me3 Deposition during Cell Differentiation.
Authors: Sanulli, S. / Justin, N. / Teissandier, A. / Ancelin, K. / Portoso, M. / Caron, M. / Michaud, A. / Lombard, B. / da Rocha, S.T. / Offer, J. / Loew, D. / Servant, N. / Wassef, M. / Burlina, F. ...Authors: Sanulli, S. / Justin, N. / Teissandier, A. / Ancelin, K. / Portoso, M. / Caron, M. / Michaud, A. / Lombard, B. / da Rocha, S.T. / Offer, J. / Loew, D. / Servant, N. / Wassef, M. / Burlina, F. / Gamblin, S.J. / Heard, E. / Margueron, R.
History
DepositionNov 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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: Polycomb protein EED
B: ALA-GLN-ARG-M3L-PHE-ALA-GLN-SER


Theoretical massNumber of molelcules
Total (without water)43,9832
Polymers43,9832
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-3 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.419, 58.144, 127.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42314.145 Da / Num. of mol.: 1 / Fragment: UNP residues 77-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530
#2: Protein/peptide ALA-GLN-ARG-M3L-PHE-ALA-GLN-SER


Mass: 1668.917 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 16463 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rsym value: 0.084 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.09 Å / Mean I/σ(I) obs: 2.23 / Rsym value: 0.365 / % possible all: 38.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIW

3iiw


Resolution: 2.3→29.072 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 837 5.08 %
Rwork0.171 --
obs0.1736 16463 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.35 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.0225 Å20 Å20 Å2
2--2.5467 Å20 Å2
3---3.4757 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 0 175 3147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073046
X-RAY DIFFRACTIONf_angle_d1.0744124
X-RAY DIFFRACTIONf_dihedral_angle_d14.5641113
X-RAY DIFFRACTIONf_chiral_restr0.079439
X-RAY DIFFRACTIONf_plane_restr0.003528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.4440.26011270.19722370X-RAY DIFFRACTION90
2.444-2.63260.25751400.1992619X-RAY DIFFRACTION99
2.6326-2.89730.29041500.19742608X-RAY DIFFRACTION100
2.8973-3.31610.23391420.17472629X-RAY DIFFRACTION99
3.3161-4.17590.17391360.14932650X-RAY DIFFRACTION99
4.1759-29.07430.20141420.15722750X-RAY DIFFRACTION97

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