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- PDB-5wp3: Crystal Structure of EED in complex with EB22 -

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Basic information

Entry
Database: PDB / ID: 5wp3
TitleCrystal Structure of EED in complex with EB22
Components
  • EB22
  • Polycomb protein EED
KeywordsGENE REGULATION / 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
Ribosome-recycling factor / Topoisomerase I; Chain A, domain 4 / 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 ...Ribosome-recycling factor / Topoisomerase I; Chain A, domain 4 / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDong, C. / Tempel, W. / Zhu, L. / Moody, J.D. / Baker, D. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor.
Authors: Moody, J.D. / Levy, S. / Mathieu, J. / Xing, Y. / Kim, W. / Dong, C. / Tempel, W. / Robitaille, A.M. / Dang, L.T. / Ferreccio, A. / Detraux, D. / Sidhu, S. / Zhu, L. / Carter, L. / Xu, C. / ...Authors: Moody, J.D. / Levy, S. / Mathieu, J. / Xing, Y. / Kim, W. / Dong, C. / Tempel, W. / Robitaille, A.M. / Dang, L.T. / Ferreccio, A. / Detraux, D. / Sidhu, S. / Zhu, L. / Carter, L. / Xu, C. / Valensisi, C. / Wang, Y. / Hawkins, R.D. / Min, J. / Moon, R.T. / Orkin, S.H. / Baker, D. / Ruohola-Baker, H.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: 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 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein EED
B: EB22


Theoretical massNumber of molelcules
Total (without water)56,43718
Polymers56,4372
Non-polymers016
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, See PDB entry 2QXV.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-11 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.070, 134.290, 61.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: 42443.324 Da / Num. of mol.: 1 / Fragment: residues 75-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Plasmid: pET28GST-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V3R / References: UniProt: O75530
#2: Protein EB22


Mass: 13993.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 16 / Source method: obtained synthetically

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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: 2.1 Å3/Da / Density % sol: 41.51 % / Mosaicity: 0.35 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG-3350, 0.2 M sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→57.07 Å / Num. obs: 17102 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 62.35 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Net I/σ(I): 14.9 / Num. measured all: 119016 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.66.71.1791272018930.6350.4861.2771.999.2
9.01-57.076.10.02726434340.9990.0120.0345.599.5

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2QXV, 3LF9. The amino acid sequence of PDB entry 3LF9 was modified with the CCP4 program CHAINSAW to match the EB22 target sequence.

2qxv

3lf9

3lf9


Resolution: 2.55→45.5 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.887 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.608 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.612 / SU Rfree Blow DPI: 0.282 / SU Rfree Cruickshank DPI: 0.285
Details: higher resolution EED structures, such as PDB entry 3K26, were used for the interpretation of poor electron density. EED backbone coordinates were restrained to a PHENIX.ROSETTA_REFINE model. ...Details: higher resolution EED structures, such as PDB entry 3K26, were used for the interpretation of poor electron density. EED backbone coordinates were restrained to a PHENIX.ROSETTA_REFINE model. Weak electron density at and around EB22 residue Leu-68 suggested a helical fold and was interpreted homologously to PDB entry 3LF9.
RfactorNum. reflection% reflection
Rfree0.244 808 5.01 %
Rwork0.204 --
obs0.206 16116 99.8 %
Displacement parametersBiso max: 139.43 Å2 / Biso mean: 53.36 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-12.4691 Å20 Å20 Å2
2---23.3634 Å20 Å2
3---10.8943 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.55→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 16 0 3408
Biso mean--28.91 --
Num. residues----462
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1127SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes518HARMONIC5
X-RAY DIFFRACTIONt_it3455HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion482SEMIHARMONIC5
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_contact3847SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3455HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4704HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion17.98
LS refinement shellResolution: 2.55→2.73 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.289 153 5.32 %
Rwork0.231 2722 -
all-2875 -
obs--99.65 %
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)
11.74710.6947-0.02972.6487-0.17371.2598-0.1669-0.0404-0.0693-0.05610.11640.0675-0.008-0.14670.0505-0.08490.0470.0047-0.0871-0.0037-0.195765.9169159.34273.5043
23.8385-0.4162-3.10592.62061.01764.121-0.0304-0.377-0.44850.4458-0.145-0.13360.19890.35380.17540.02060.0792-0.0647-0.11380.0734-0.141272.0456145.92492.9666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A77 - 441
2X-RAY DIFFRACTION2{ B|* }B1 - 112

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