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- PDB-7si5: CRYSTAL STRUCTURE OF EED WITH MRTX-1919 -

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Basic information

Entry
Database: PDB / ID: 7si5
TitleCRYSTAL STRUCTURE OF EED WITH MRTX-1919
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 / 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
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
Similarity search - Domain/homology
Chem-9L0 / FORMIC ACID / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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-1919
Authors: Burns, A.C.
History
DepositionOct 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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)47,33019
Polymers46,1581
Non-polymers1,17218
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.860, 85.030, 91.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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 / Plasmid: PEMB32_BSA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON PLUS(DE3) RIL / References: UniProt: O75530

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Non-polymers , 5 types, 387 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-9L0 / (4R)-8-(1,3-dimethyl-1H-pyrazol-5-yl)-5-{[(5-fluoro-2,3-dihydro-1-benzofuran-4-yl)methyl]amino}imidazo[1,2-c]pyrimidine-2-carbonitrile / MRTX-1919


Mass: 403.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18FN7O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 3.1 mM Sodium Formate, 100 mM Hepes pH 7.5, seeding

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2017
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→49 Å / Num. obs: 46304 / % possible obs: 99.7 % / Redundancy: 6.03 % / Biso Wilson estimate: 27.06 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.01
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 2996 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIXDEV_2890refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BE4 MODEL

Resolution: 1.75→48.97 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.187 1955 4.22 %RANDOM, 0
Rwork0.151 ---
obs0.153 46300 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.39 Å2 / Biso mean: 10.83 Å2 / Biso min: 0.03 Å2
Refinement stepCycle: final / Resolution: 1.75→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 79 377 3337
Biso mean--38.32 37.84 -
Num. residues----361
LS refinement shellResolution: 1.75→1.79 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2798 170 -
Rwork0.2411 2996 -
all-3166 -
obs--97 %
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)
12.95530.03850.34622.8211-0.25963.27910.018-0.03120.10470.10750.0211-0.2358-0.07490.1779-0.04040.1676-0.0111-0.00050.1043-0.03840.17991.7798-18.13726.0384
20.64310.8310.62072.1030.27422.58070.0082-0.02560.0920.2399-0.00720.0676-0.0116-0.0275-0.00390.15110.01460.01420.1167-0.01180.1689-3.7112-12.183524.052
30.58120.38010.18261.81710.31041.1176-0.0072-0.00410.07040.00450.01650.1029-0.0584-0.0571-0.01070.07350.0090.00070.12090.0190.1339-11.6343-19.60418.6764
43.3313-2.04010.15458.1347-0.42521.99940.0780.1180.3167-0.3203-0.0725-0.0132-0.07930.1366-0.00880.1178-0.0086-0.02610.17420.03230.1386-14.4581-12.8125-7.1802
51.9945-0.81441.83672.1907-1.13363.17190.05980.0561-0.0924-0.0609-0.02140.08570.2264-0.0388-0.03880.1431-0.02740.00380.1343-0.00220.1605-9.9455-38.06918.9217
60.7552-0.1166-0.07041.85130.16251.43730.03750.0006-0.01170.0943-0.036-0.04240.0487-0.0079-0.0060.1232-0.00280.0040.09710.02340.1084-1.1155-36.379120.7859
72.2221.9182-0.91142.6216-1.1664.56470.07840.0297-0.14730.0462-0.0266-0.23370.04230.1751-0.06770.16810.0225-0.0080.1018-0.00470.15812.9169-23.629827.0436
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0
2X-RAY DIFFRACTION2A0
3X-RAY DIFFRACTION3A0
4X-RAY DIFFRACTION4A0
5X-RAY DIFFRACTION5A0
6X-RAY DIFFRACTION6A0
7X-RAY DIFFRACTION7A0

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