[English] 日本語
Yorodumi
- PDB-6yvi: EED in complex with a cyano-benzofuran -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yvi
TitleEED in complex with a cyano-benzofuran
ComponentsPolycomb protein EED
KeywordsPROTEIN BINDING / Methyl transferase 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-L9W / Chem-PV5 / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsRead, J.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Free energy perturbation in the design of EED ligands as inhibitors of polycomb repressive complex 2 (PRC2) methyltransferase.
Authors: O' Donovan, D.H. / Gregson, C. / Packer, M.J. / Greenwood, R. / Pike, K.G. / Kawatkar, S. / Bloecher, A. / Robinson, J. / Read, J. / Code, E. / Hsu, J.H. / Shen, M. / Woods, H. / Barton, P. ...Authors: O' Donovan, D.H. / Gregson, C. / Packer, M.J. / Greenwood, R. / Pike, K.G. / Kawatkar, S. / Bloecher, A. / Robinson, J. / Read, J. / Code, E. / Hsu, J.H. / Shen, M. / Woods, H. / Barton, P. / Fillery, S. / Williamson, B. / Rawlins, P.B. / Bagal, S.K.
History
DepositionApr 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 2.0Jul 14, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_refine_tls_group
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _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 / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_refine_tls_group.selection_details
Revision 2.1Jan 24, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,4615
Polymers84,5982
Non-polymers8633
Water5,242291
1
A: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7613
Polymers42,2991
Non-polymers4622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polycomb protein EED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7012
Polymers42,2991
Non-polymers4011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.888, 86.528, 97.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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.: 1 / 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-PV5 / 5-fluoranyl-4-[[[8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-yl]amino]methyl]-2,3-dihydro-1-benzofuran-7-carbonitrile


Mass: 401.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16FN7O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15M CaCl2, 18% PEG 3350, 0.1M PCPT pH 8.3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.26→64.36 Å / Num. obs: 23221 / % possible obs: 92.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.65 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.7
Reflection shellResolution: 2.26→2.5 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1161 / CC1/2: 0.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SFB

6sfb


Resolution: 2.26→64.36 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.314
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1194 5.14 %RANDOM
Rwork0.182 ---
obs0.185 23221 67.2 %-
Displacement parametersBiso max: 132.87 Å2 / Biso mean: 35.62 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1--2.5818 Å20 Å20 Å2
2--4.5356 Å20 Å2
3----1.9538 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.26→64.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5513 0 61 291 5865
Biso mean--32.87 34.66 -
Num. residues----694
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1933SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes831HARMONIC5
X-RAY DIFFRACTIONt_it5719HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
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_contact6584SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5719HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7771HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion18.92
LS refinement shellResolution: 2.26→2.36 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.314 4 4 %
Rwork0.232 96 -
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)
11.5738-0.1352-0.05481.1334-0.1781.1167-0.02870.0850.147-0.04940.02940.0730.0171-0.0545-0.0006-0.0919-0.0196-0.0263-0.0026-0.0024-0.110825.655233.64996.0252
22.86580.01210.08311.2201-0.49552.05340.0037-0.2323-0.10510.0602-0.1562-0.0518-0.08270.30890.1525-0.1308-0.05890.017-0.05780.0072-0.1012-23.627742.850316.7174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|82 - A|439 }A82 - 439
2X-RAY DIFFRACTION2{ B|81 - B|439 }B81 - 439

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more