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- PDB-5ttw: Crystal Structure of EED in Complex with UNC4859 -

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Basic information

Entry
Database: PDB / ID: 5ttw
TitleCrystal Structure of EED in Complex with UNC4859
Components
  • Polycomb protein EED
  • UNC4859
KeywordsTRANSCRIPTION REGULATOR/INHIBITOR / WD40 / EED peptide inhibitor / TRANSCRIPTION REGULATOR-INHIBITOR complex
Function / homology
Function and homology information


ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / enzyme activator activity / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / PKMTs methylate histone lysines ...ESC/E(Z) complex / spinal cord development / histone methyltransferase activity / Transcriptional Regulation by E2F6 / 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 / chromatin binding / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsThe, J. / Barnash, K.D. / Brown, P.J. / Edwards, A.M. / Bountra, C. / Frye, S.V. / James, L.I. / Arrowsmith, C.H.
CitationJournal: ACS Comb Sci / Year: 2017
Title: Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2.
Authors: Barnash, K.D. / The, J. / Norris-Drouin, J.L. / Cholensky, S.H. / Worley, B.M. / Li, F. / Stuckey, J.I. / Brown, P.J. / Vedadi, M. / Arrowsmith, C.H. / Frye, S.V. / James, L.I.
History
DepositionNov 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein EED
B: UNC4859
C: Polycomb protein EED
D: UNC4859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,17028
Polymers85,9784
Non-polymers19224
Water10,683593
1
A: Polycomb protein EED
B: UNC4859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,08514
Polymers42,9892
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-21 kcal/mol
Surface area15310 Å2
MethodPISA
2
C: Polycomb protein EED
D: UNC4859
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,08514
Polymers42,9892
Non-polymers9612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-18 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.486, 56.212, 76.687
Angle α, β, γ (deg.)90.000, 105.330, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42356.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus RIL / References: UniProt: O75530
#2: Protein/peptide UNC4859


Mass: 632.814 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was synthesized to mimic the JARID2 peptide ligand of EED
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 2.13 Å3/Da / Density % sol: 42.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 5.5
Details: 20% PEG3350, 0.1 M ammonium sulfate, 0.1M Bis Tris pH 5.5
Temp details: set up at room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2016 / Details: bent cylinders mirrors
RadiationMonochromator: cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.74→85.1 Å / Num. obs: 74365 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.069 / Rrim(I) all: 0.134 / Net I/σ(I): 8.5 / Num. measured all: 274004 / Scaling rejects: 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.74-1.773.41.4750.282195.6
9.04-85.13.50.0340.998199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.27data scaling
MOLREPphasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3K26

3k26


Resolution: 1.74→85.1 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.3 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.117 / Details: Molecular replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 3762 5.1 %RANDOM
Rwork0.1669 ---
obs0.1693 70602 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.09 Å2 / Biso mean: 22.301 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.43 Å2
2--0.26 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.74→85.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5808 0 32 593 6433
Biso mean--29.56 33 -
Num. residues----733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196293
X-RAY DIFFRACTIONr_bond_other_d0.0020.025713
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9288589
X-RAY DIFFRACTIONr_angle_other_deg1.056313127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1555794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80123.645299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.712151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2521540
X-RAY DIFFRACTIONr_chiral_restr0.120.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027359
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021577
X-RAY DIFFRACTIONr_mcbond_it2.1752.0793100
X-RAY DIFFRACTIONr_mcbond_other2.1752.0793101
X-RAY DIFFRACTIONr_mcangle_it3.1383.0933923
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 266 -
Rwork0.336 5054 -
all-5320 -
obs--97.26 %

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