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- PDB-5u5k: Crystal structure of EED in complex with 3-(3-methoxybenzyl)piper... -

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Basic information

Entry
Database: PDB / ID: 5u5k
TitleCrystal structure of EED in complex with 3-(3-methoxybenzyl)piperidine hydrochloride
ComponentsPolycomb protein EED
KeywordsTRANSCRIPTION / EED / fragment-based generation / oncology
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
(3R)-3-[(3-methoxyphenyl)methyl]piperidine / FORMIC ACID / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.33 Å
AuthorsBussiere, D. / Shu, W.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.
Authors: Lingel, A. / Sendzik, M. / Huang, Y. / Shultz, M.D. / Cantwell, J. / Dillon, M.P. / Fu, X. / Fuller, J. / Gabriel, T. / Gu, J. / Jiang, X. / Li, L. / Liang, F. / McKenna, M. / Qi, W. / Rao, ...Authors: Lingel, A. / Sendzik, M. / Huang, Y. / Shultz, M.D. / Cantwell, J. / Dillon, M.P. / Fu, X. / Fuller, J. / Gabriel, T. / Gu, J. / Jiang, X. / Li, L. / Liang, F. / McKenna, M. / Qi, W. / Rao, W. / Sheng, X. / Shu, W. / Sutton, J. / Taft, B. / Wang, L. / Zeng, J. / Zhang, H. / Zhang, M. / Zhao, K. / Lindvall, M. / Bussiere, D.E.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)42,6083
Polymers42,3561
Non-polymers2512
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.661, 60.833, 66.055
Angle α, β, γ (deg.)90.00, 104.56, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 1 / Fragment: UNP residues 76-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: O75530
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-7VY / (3R)-3-[(3-methoxyphenyl)methyl]piperidine


Mass: 205.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 291 K / Method: evaporation
Details: Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 Celsius and harvested and soaked in defined drops ...Details: Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 Celsius and harvested and soaked in defined drops consisting of 30 uL of precipitant with 1-2 mM of compound (typically solubilized in DMSO) for 24-48 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 3.5 M sodium formate, 1-2 mM of compound, and 30% (v/v) glycerol.

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→44.71 Å / Num. obs: 15667 / % possible obs: 93.2 % / Redundancy: 6.1 % / Biso Wilson estimate: 55.52 Å2 / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementResolution: 2.33→44.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.374 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.236
RfactorNum. reflection% reflectionSelection details
Rfree0.225 764 4.89 %RANDOM
Rwork0.163 ---
obs0.166 15618 93.1 %-
Displacement parametersBiso mean: 52.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.9165 Å20 Å2-0.2645 Å2
2---0.0271 Å20 Å2
3----0.8895 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 2.33→44.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 18 155 3026
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012943HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.173993HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d997SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes427HARMONIC5
X-RAY DIFFRACTIONt_it2943HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion19.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion381SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3272SEMIHARMONIC4
LS refinement shellResolution: 2.33→2.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.262 143 5.12 %
Rwork0.192 2649 -
all0.195 2792 -
obs--92.68 %
Refinement TLS params.Method: refined / Origin x: 18.8869 Å / Origin y: -10.1516 Å / Origin z: 17.318 Å
111213212223313233
T-0.0916 Å2-0.0434 Å2-0.0132 Å2--0.1579 Å20.0577 Å2---0.1292 Å2
L3.0469 °20.2126 °2-0.3637 °2-1.683 °20.5111 °2--1.5113 °2
S-0.1634 Å °0.3027 Å °0.2217 Å °-0.2255 Å °0.1331 Å °0.1188 Å °-0.0227 Å °-0.0134 Å °0.0303 Å °
Refinement TLS groupSelection details: { A|* }

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