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- PDB-7si4: CRYSTAL STRUCTURE OF EED WITH MRTX-2219 -

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Basic information

Entry
Database: PDB / ID: 7si4
TitleCRYSTAL STRUCTURE OF EED WITH MRTX-2219
ComponentsPolycomb protein EED
KeywordsGENE REGULATION / EED / ONCOLOGY / TRANSCRIPTION-TRANSFERASE
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-9JL / FORMIC ACID / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGunn, R.J. / Burns, A.C. / Lawson, J.D. / Marx, M.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: TO BE PUBLISHED
Title: CRYSTAL STRUCTURE OF EED WITH MRTX-2219
Authors: Burns, A.C.
History
DepositionOct 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7074
Polymers46,1581
Non-polymers5493
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.658, 85.279, 91.236
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: 46158.348 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-9JL / (4S)-8-{4-[(dimethylamino)methyl]-2-methylphenyl}-5-{[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]amino}imidazo[1,2-c]pyrimidine-2-carbonitrile / MRTX-2219


Mass: 456.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25FN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 3.5 M Sodium Formate, 50 mM 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30316 / % possible obs: 83.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 37.11 Å2 / CC1/2: 0.97 / Rsym value: 0.12 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.96 Å / Num. unique obs: 728 / CC1/2: 0.37

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JZH

3jzh


Resolution: 1.9→34.28 Å / SU ML: 0.2481 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3401
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 1556 5.13 %
Rwork0.1715 28760 -
obs0.1736 30316 83.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 40 323 3240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473012
X-RAY DIFFRACTIONf_angle_d0.73834097
X-RAY DIFFRACTIONf_chiral_restr0.0529438
X-RAY DIFFRACTIONf_plane_restr0.0053523
X-RAY DIFFRACTIONf_dihedral_angle_d12.8221078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.3825430.365728X-RAY DIFFRACTION23.74
1.96-2.030.3518790.34541587X-RAY DIFFRACTION51.26
2.03-2.110.36511340.30522177X-RAY DIFFRACTION71.11
2.11-2.210.28031350.27722560X-RAY DIFFRACTION82.62
2.21-2.320.28621820.22423046X-RAY DIFFRACTION98.66
2.32-2.470.24731640.20713078X-RAY DIFFRACTION99.17
2.47-2.660.24681820.18663068X-RAY DIFFRACTION98.48
2.66-2.920.23391470.18923088X-RAY DIFFRACTION97.76
2.92-3.350.23491610.16223007X-RAY DIFFRACTION95.97
3.35-4.220.15161750.13253164X-RAY DIFFRACTION99.4
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)
10.871585557886-0.008141300355520.8874851002462.89300350483-0.3077056022183.00292043240.0114253855922-0.0423211015660.02365636144850.1574143850910.05757857080870.172282810724-0.1643889819870.0011611180869-0.04663725662860.2196764813030.009554155161310.01369366247220.23961618709-0.01288549090090.291472157893-6.21712220709-14.442867564916.9095945408
21.86304915376-0.991810537010.8499130041592.75881888586-1.687429501632.039098857580.188196704121-0.0112704997659-0.250919482748-0.492449634054-0.01972421787830.5603405798420.394683158346-0.0742654276756-0.1164088758540.371767990733-0.0201393176209-0.1160006130210.260762564791-0.02354435786090.362172133549-11.5107038765-30.34922174774.28883625941
31.37431560114-0.523229288750.4425802143032.546960447610.0371788053241.258333903320.0859500424432-0.0455216996697-0.236353610855-0.1831664500470.0540784178610.4718908661710.226374976894-0.136052997458-0.09501310887910.369423105148-0.0280887482929-0.02387275963670.3120698745110.05445234221320.38944053927-4.4266558305-36.100504337318.3144889427
40.8077445706130.3356178202170.03554917004453.07054776151-0.3988356712421.223882152620.0578628765765-0.104528670910.02595702829120.418213517975-0.0227478832156-0.3145949586650.06304067344450.0655207955268-0.01431061344540.3515808468890.0137755539783-0.01858100415380.3406540066640.03881759188730.2915529836053.78415116924-29.91858030626.0935189506
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 81 through 229 )81 - 2291 - 149
22chain 'A' and (resid 230 through 342 )230 - 342150 - 262
33chain 'A' and (resid 343 through 385 )343 - 385263 - 305
44chain 'A' and (resid 386 through 440 )386 - 440306 - 360

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