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- PDB-6v3x: Crystal structure of EED in complex with PALI1-K1241me3 peptide -

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Basic information

Entry
Database: PDB / ID: 6v3x
TitleCrystal structure of EED in complex with PALI1-K1241me3 peptide
Components
  • PALI1 peptide
  • Polycomb protein EED
KeywordsGENE REGULATION / EED / PALI1 / LCOR / C10ORF12 / tri-methyl-lysine
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 / heterochromatin formation ...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 / heterochromatin formation / 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
: / 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
Similarity search - Domain/homology
Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, Q. / Davidovich, C.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE180100219 Australia
Australian Research Council (ARC)DP190103407 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1162921 Australia
Citation
Journal: Nat Commun / Year: 2021
Title: PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis.
Authors: Zhang, Q. / Agius, S.C. / Flanigan, S.F. / Uckelmann, M. / Levina, V. / Owen, B.M. / Davidovich, C.
#1: Journal: Nat Commun / Year: 2021
Title: PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis
Authors: Zhang, Q. / Aguis, S.C. / Flanigan, S.F. / Uckelmann, M. / Levina, V. / Owen, B.M. / Davidovich, C.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: 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: PALI1 peptide


Theoretical massNumber of molelcules
Total (without water)43,0892
Polymers43,0892
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-5 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.243, 84.721, 90.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 42356.246 Da / Num. of mol.: 1 / Fragment: UNP residues 81-440
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 PALI1 peptide


Mass: 732.953 Da / Num. of mol.: 1 / Fragment: residues 1239-1244 / Source method: obtained synthetically / Details: UNP Q96JN0-3 / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.6 M sodium formate, 10 mM TCEP, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.7→47.76 Å / Num. obs: 47118 / % possible obs: 97.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Net I/σ(I): 16.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8 % / Rmerge(I) obs: 0.631 / Num. unique obs: 6664 / CC1/2: 0.898 / Rpim(I) all: 0.234 / Rrim(I) all: 0.674 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.17.1_3660refinement
XDSdata processing
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IIW

3iiw


Resolution: 1.7→35.24 Å / SU ML: 0.1323 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 2291 4.87 %
Rwork0.1737 44749 -
obs0.175 47040 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 0 178 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582965
X-RAY DIFFRACTIONf_angle_d0.83814036
X-RAY DIFFRACTIONf_chiral_restr0.0599439
X-RAY DIFFRACTIONf_plane_restr0.005518
X-RAY DIFFRACTIONf_dihedral_angle_d14.2308400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25671500.22182682X-RAY DIFFRACTION96.23
1.74-1.780.22521380.20232721X-RAY DIFFRACTION96.1
1.78-1.820.26971560.19362734X-RAY DIFFRACTION96.59
1.82-1.870.22311480.18662719X-RAY DIFFRACTION96.6
1.87-1.930.22771330.19222749X-RAY DIFFRACTION96.65
1.93-1.990.19561400.17282727X-RAY DIFFRACTION96.92
1.99-2.060.20571310.17362797X-RAY DIFFRACTION97.31
2.06-2.140.16681460.16252757X-RAY DIFFRACTION97.38
2.14-2.240.20571320.16472782X-RAY DIFFRACTION97.43
2.24-2.360.21881490.18372808X-RAY DIFFRACTION97.75
2.36-2.50.24441510.18412798X-RAY DIFFRACTION98.53
2.5-2.70.2171350.19292822X-RAY DIFFRACTION97.72
2.7-2.970.24881170.19962865X-RAY DIFFRACTION98.45
2.97-3.40.19611400.17812877X-RAY DIFFRACTION98.89
3.4-4.280.18541280.15242943X-RAY DIFFRACTION99
4.28-35.240.16311970.15652968X-RAY DIFFRACTION98.26

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