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- PDB-3ijc: Crystal structure of Eed in complex with NDSB-195 -

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Basic information

Entry
Database: PDB / ID: 3ijc
TitleCrystal structure of Eed in complex with NDSB-195
ComponentsPolycomb 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 / 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
ETHYL DIMETHYL AMMONIO PROPANE SULFONATE / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 4, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3352
Polymers42,1401
Non-polymers1951
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.803, 85.337, 91.231
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: 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: Chemical ChemComp-NDS / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE


Mass: 195.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
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: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
Details: Vertically collimating premirror, double crystal Si(111) monochromator with sagital focussing, vertical focusing mirror
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 31920 / Num. obs: 31920 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 14.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.426 / % possible all: 91

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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: 1.95→27.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.69 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23156 1680 5.1 %RANDOM
Rwork0.19539 ---
all0.19724 31442 --
obs0.19724 31442 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.715 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 12 238 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212979
X-RAY DIFFRACTIONr_angle_refined_deg1.681.934036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24223.767146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36915512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3691519
X-RAY DIFFRACTIONr_chiral_restr0.1190.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022257
X-RAY DIFFRACTIONr_nbd_refined0.2040.21149
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.28
X-RAY DIFFRACTIONr_mcbond_it1.151.51867
X-RAY DIFFRACTIONr_mcangle_it1.78222873
X-RAY DIFFRACTIONr_scbond_it2.73731348
X-RAY DIFFRACTIONr_scangle_it4.0874.51163
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 115 -
Rwork0.269 2113 -
obs--90.57 %

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