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- PDB-5k0m: Targeting the PRC2 complex through a novel protein-protein intera... -

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Basic information

Entry
Database: PDB / ID: 5k0m
TitleTargeting the PRC2 complex through a novel protein-protein interaction inhibitor of EED
ComponentsPolycomb protein EED
KeywordsPROTEIN BINDING / WD40 PRC2
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
Chem-6PU / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJakob, C.G. / Bigelow, L.J. / Zhu, H. / Sun, C.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: The EED protein-protein interaction inhibitor A-395 inactivates the PRC2 complex.
Authors: He, Y. / Selvaraju, S. / Curtin, M.L. / Jakob, C.G. / Zhu, H. / Comess, K.M. / Shaw, B. / The, J. / Lima-Fernandes, E. / Szewczyk, M.M. / Cheng, D. / Klinge, K.L. / Li, H.Q. / Pliushchev, M. ...Authors: He, Y. / Selvaraju, S. / Curtin, M.L. / Jakob, C.G. / Zhu, H. / Comess, K.M. / Shaw, B. / The, J. / Lima-Fernandes, E. / Szewczyk, M.M. / Cheng, D. / Klinge, K.L. / Li, H.Q. / Pliushchev, M. / Algire, M.A. / Maag, D. / Guo, J. / Dietrich, J. / Panchal, S.C. / Petros, A.M. / Sweis, R.F. / Torrent, M. / Bigelow, L.J. / Senisterra, G. / Li, F. / Kennedy, S. / Wu, Q. / Osterling, D.J. / Lindley, D.J. / Gao, W. / Galasinski, S. / Barsyte-Lovejoy, D. / Vedadi, M. / Buchanan, F.G. / Arrowsmith, C.H. / Chiang, G.G. / Sun, C. / Pappano, W.N.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2023Group: 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

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Assembly

Deposited unit
A: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4242
Polymers42,9371
Non-polymers4871
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.843, 84.911, 91.627
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: 42936.922 Da / Num. of mol.: 1
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: Chemical ChemComp-6PU / (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-{4-[4-(methylsulfonyl)piperazin-1-yl]phenyl}pyrrolidin-3-amine


Mass: 486.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H35FN4O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 8.5
Details: 3.08M Sodium Formate, 20% Glycerol, 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.828→48.92 Å / Num. obs: 40632 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.141 / Net I/σ(I): 12.7
Reflection shellResolution: 1.828→1.834 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.145 / Mean I/σ(I) obs: 2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JZN

3jzn


Resolution: 1.83→48.912 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.647 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18475 1997 4.9 %RANDOM
Rwork0.13344 ---
obs0.13598 38572 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.83→48.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 34 366 3306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193032
X-RAY DIFFRACTIONr_bond_other_d0.0020.022829
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9244116
X-RAY DIFFRACTIONr_angle_other_deg1.23936507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6185362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36923.784148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3251520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023485
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02741
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5871.9191440
X-RAY DIFFRACTIONr_mcbond_other1.5871.9171438
X-RAY DIFFRACTIONr_mcangle_it1.9532.8811798
X-RAY DIFFRACTIONr_mcangle_other1.9522.8811799
X-RAY DIFFRACTIONr_scbond_it2.8122.3551592
X-RAY DIFFRACTIONr_scbond_other2.8112.3561593
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9433.3552317
X-RAY DIFFRACTIONr_long_range_B_refined4.48617.6493610
X-RAY DIFFRACTIONr_long_range_B_other3.70616.7493444
X-RAY DIFFRACTIONr_rigid_bond_restr9.44235861
X-RAY DIFFRACTIONr_sphericity_free34.8545135
X-RAY DIFFRACTIONr_sphericity_bonded7.92556012
LS refinement shellResolution: 1.828→1.876 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 162 -
Rwork0.264 2786 -
obs--99.53 %

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