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- PDB-7kxt: Crystal structure of human EED -

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Basic information

Entry
Database: PDB / ID: 7kxt
TitleCrystal structure of human EED
ComponentsPolycomb protein EED
KeywordsGENE REGULATION / EED / WD40 / Structural Genomics / Structural Genomics Consortium / SGC
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-XB7 / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhu, L. / Dong, A. / Du, D. / Liu, Y. / Luo, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Guided Development of Small-Molecule PRC2 Inhibitors Targeting EZH2-EED Interaction.
Authors: Du, D. / Xu, D. / Zhu, L. / Stazi, G. / Zwergel, C. / Liu, Y. / Luo, Z. / Li, Y. / Zhang, Y. / Zhu, K. / Ding, Y. / Liu, J. / Fan, S. / Zhao, K. / Zhang, N. / Kong, X. / Jiang, H. / Chen, K. ...Authors: Du, D. / Xu, D. / Zhu, L. / Stazi, G. / Zwergel, C. / Liu, Y. / Luo, Z. / Li, Y. / Zhang, Y. / Zhu, K. / Ding, Y. / Liu, J. / Fan, S. / Zhao, K. / Zhang, N. / Kong, X. / Jiang, H. / Chen, K. / Zhao, K. / Valente, S. / Min, J. / Duan, W. / Luo, C.
History
DepositionDec 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)93,23456
Polymers92,3172
Non-polymers91754
Water1,76598
1
A: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,61729
Polymers46,1581
Non-polymers45928
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,61727
Polymers46,1581
Non-polymers45926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.470, 49.940, 105.320
Angle α, β, γ (deg.)90.000, 105.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 80 through 81 and (name N...
21(chain B and ((resid 80 through 81 and (name N...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRSERSER(chain A and ((resid 80 through 81 and (name N...AA80 - 8141 - 42
12LYSLYSARGARG(chain A and ((resid 80 through 81 and (name N...AA77 - 44138 - 402
13LYSLYSARGARG(chain A and ((resid 80 through 81 and (name N...AA77 - 44138 - 402
14LYSLYSARGARG(chain A and ((resid 80 through 81 and (name N...AA77 - 44138 - 402
15LYSLYSARGARG(chain A and ((resid 80 through 81 and (name N...AA77 - 44138 - 402
21TYRTYRSERSER(chain B and ((resid 80 through 81 and (name N...BB80 - 8141 - 42
22TYRTYRLEULEU(chain B and ((resid 80 through 81 and (name N...BB80 - 44041 - 401
23TYRTYRLEULEU(chain B and ((resid 80 through 81 and (name N...BB80 - 44041 - 401
24TYRTYRLEULEU(chain B and ((resid 80 through 81 and (name N...BB80 - 44041 - 401
25TYRTYRLEULEU(chain B and ((resid 80 through 81 and (name N...BB80 - 44041 - 401

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Plasmid: pET28GST-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75530
#2: Chemical ChemComp-XB7 / 1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine


Mass: 458.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31FN4O
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 52 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.1 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.5M Sodium Formate, 0.1M TrisCl pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 12, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.15→40.392 Å / Num. obs: 44346 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.97 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.066 / Rrim(I) all: 0.123 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.213.10.813966031220.5030.5410.9821.494.6
9.62-40.392.90.03515685330.9960.0240.04324.196.7

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JZN

3jzn


Resolution: 2.15→40.39 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 2165 4.88 %
Rwork0.178 42169 -
obs0.1798 44334 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.34 Å2 / Biso mean: 40.7572 Å2 / Biso min: 14.42 Å2
Refinement stepCycle: final / Resolution: 2.15→40.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5682 0 120 98 5900
Biso mean--43.74 35.88 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086029
X-RAY DIFFRACTIONf_angle_d0.9328212
X-RAY DIFFRACTIONf_chiral_restr0.06890
X-RAY DIFFRACTIONf_plane_restr0.0061052
X-RAY DIFFRACTIONf_dihedral_angle_d13.7913571
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3222X-RAY DIFFRACTION5.038TORSIONAL
12B3222X-RAY DIFFRACTION5.038TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.20.32361460.2797263994
2.2-2.2550.29781480.2452280699
2.255-2.3160.27341630.23862776100
2.316-2.38420.26491360.2345285499
2.3842-2.46110.27891480.2249277999
2.4611-2.5490.27621610.2138271797
2.549-2.65110.26541520.2071282899
2.6511-2.77170.28131280.2115284299
2.7717-2.91780.21871470.184281999
2.9178-3.10060.22171270.1796281298
3.1006-3.33980.21681570.1652276598
3.3398-3.67570.18771340.1594286199
3.6757-4.20720.17751390.1429283499
4.2072-5.29870.1481370.1324289199
5.2987-40.390.21291420.19294699
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)
10.97890.01250.39851.43640.27371.4181-0.01160.13770.07190.0341-0.0074-0.2835-0.04930.37080.00370.1815-0.0257-0.00960.25310.03440.2285-9.414-5.764-44.189
21.3465-0.519-0.26581.4050.04140.9438-0.0072-0.1810.03460.0783-0.009-0.2256-0.00780.2050.01920.1942-0.0112-0.01020.20460.0190.2024-22.332-15.4292.952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 77:441 )A77 - 441
2X-RAY DIFFRACTION2( CHAIN B AND RESID 80:440 )B80 - 440

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