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- PDB-6sfc: EED in complex with a methyl-thiazole -

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Basic information

Entry
Database: PDB / ID: 6sfc
TitleEED in complex with a methyl-thiazole
ComponentsPolycomb protein EED
KeywordsPROTEIN BINDING / Methyltransferase EED PRC2 epigenetic H3K27 WD40 Inhibitor
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
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
Similarity search - Domain/homology
Chem-L9T / Chem-L9W / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRead, J.A.
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Rapid Identification of Novel Allosteric PRC2 Inhibitors.
Authors: Read, J.A. / Tart, J. / Rawlins, P.B. / Gregson, C. / Jones, K. / Gao, N. / Zhu, X. / Tomlinson, R. / Code, E. / Cheung, T. / Chen, H. / Kawatkar, S.P. / Bloecher, A. / Bagal, S. / O'Donovan, D.H. / Robinson, J.
History
DepositionAug 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 14, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein EED
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4286
Polymers84,5982
Non-polymers8304
Water7,152397
1
A: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8014
Polymers42,2991
Non-polymers5023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6282
Polymers42,2991
Non-polymers3281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.000, 86.180, 97.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 42299.195 Da / Num. of mol.: 2
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-L9W / N-(2,3-dihydro-1-benzofuran-4-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine


Mass: 421.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19N5O3S
#4: Chemical ChemComp-L9T / N-(1,3-benzodioxol-4-ylmethyl)-4-methyl-5-(1-methylpyrazol-3-yl)-1,3-thiazol-2-amine


Mass: 328.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 23% PEG3350, 0.1 M PCTP pH 8.5, 200 mM MgCl2, 10 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→48.6 Å / Num. obs: 49548 / % possible obs: 99.3 % / Redundancy: 3.3 % / CC1/2: 0.998 / Net I/σ(I): 12
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 21468 / CC1/2: 0.856

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.59 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.158
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2475 5 %RANDOM
Rwork0.192 ---
obs0.194 49484 99.5 %-
Displacement parametersBiso max: 161.19 Å2 / Biso mean: 49.41 Å2 / Biso min: 21.79 Å2
Baniso -1Baniso -2Baniso -3
1--4.2039 Å20 Å20 Å2
2--9.8797 Å20 Å2
3----5.6758 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5496 0 55 397 5948
Biso mean--49.78 50.94 -
Num. residues----694
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1917SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes963HARMONIC5
X-RAY DIFFRACTIONt_it5694HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion737SEMIHARMONIC5
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_contact6652SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5694HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7740HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion18.07
LS refinement shellResolution: 2→2.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2907 50 5.05 %
Rwork0.2548 940 -
all0.2565 990 -
obs--81.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1050.04470.1561.8691-0.21090.91440.05190.0955-0.1022-0.1086-0.01860.2010.01450.0176-0.0333-0.15280.0248-0.0057-0.2096-0.0322-0.132531.070247.292230.3629
21.8844-0.27880.83293.5048-0.35812.6311-0.2693-0.14790.19480.48380.0013-0.1678-0.5308-0.11750.268-0.07150.0703-0.0288-0.23270.0008-0.097521.9475-2.154641.0861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A82 - 439
2X-RAY DIFFRACTION2{ B|* }B81 - 439

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