[English] 日本語
Yorodumi
- PDB-5u5h: Crystal structure of EED in complex with 6-(2-fluoro-5-methoxyben... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u5h
TitleCrystal structure of EED in complex with 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine 6-(2-fluoro-5-methoxybenzyl)-1-isopropyl-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine
ComponentsPolycomb protein EED
KeywordsTRANSCRIPTION / EED / fragment-based generation / oncology
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
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 ...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 / Mainly Beta
Similarity search - Domain/homology
Chem-7VV / Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBussiere, D. / Shu, W.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase.
Authors: Lingel, A. / Sendzik, M. / Huang, Y. / Shultz, M.D. / Cantwell, J. / Dillon, M.P. / Fu, X. / Fuller, J. / Gabriel, T. / Gu, J. / Jiang, X. / Li, L. / Liang, F. / McKenna, M. / Qi, W. / Rao, ...Authors: Lingel, A. / Sendzik, M. / Huang, Y. / Shultz, M.D. / Cantwell, J. / Dillon, M.P. / Fu, X. / Fuller, J. / Gabriel, T. / Gu, J. / Jiang, X. / Li, L. / Liang, F. / McKenna, M. / Qi, W. / Rao, W. / Sheng, X. / Shu, W. / Sutton, J. / Taft, B. / Wang, L. / Zeng, J. / Zhang, H. / Zhang, M. / Zhao, K. / Lindvall, M. / Bussiere, D.E.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7663
Polymers42,3561
Non-polymers4092
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.570, 60.000, 66.570
Angle α, β, γ (deg.)90.00, 103.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Polycomb protein EED / hEED / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 42356.246 Da / Num. of mol.: 1 / Fragment: UNP residues 76-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: O75530
#2: Chemical ChemComp-7VV / (6S)-6-[(2-fluoro-5-methoxyphenyl)methyl]-1-(propan-2-yl)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-3-amine


Mass: 317.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24FN3O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 291 K / Method: evaporation
Details: Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 degree Celsius and harvested and soaked in defined drops ...Details: Crystals grown in a precipitant composed of 3-3.5 M sodium formate using the vapor diffusion method. Crystals grew in 3-5 days at 18 degree Celsius and harvested and soaked in defined drops consisting of 30 uL of precipitant with 1-2 mM of compound (typically solubilized in DMSO) for 24-48 h. Crystals were cryopreserved for data collection using a cryosolution consisting of 3.5 M sodium formate, 1-2 mM of compound, and 30% (v/v) glycerol.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 1.8→64.63 Å / Num. obs: 34983 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 24.85 Å2 / Net I/σ(I): 6.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.113
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1742 4.98 %RANDOM
Rwork0.164 ---
obs0.166 34960 97.1 %-
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.2689 Å20 Å2-4.4565 Å2
2--0.5519 Å20 Å2
3----0.283 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.8→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 29 338 3231
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013056HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094177HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1059SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes443HARMONIC5
X-RAY DIFFRACTIONt_it3056HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion17.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion384SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3737SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.249 120 4.26 %
Rwork0.23 2698 -
all0.231 2818 -
obs--95.91 %
Refinement TLS params.Method: refined / Origin x: -1.623 Å / Origin y: 0.2417 Å / Origin z: 14.6686 Å
111213212223313233
T-0.0146 Å20.0151 Å20.0253 Å2--0.1245 Å2-0.0265 Å2---0.0796 Å2
L1.214 °2-0.1139 °2-0.4593 °2-0.956 °2-0.1349 °2--1.1213 °2
S-0.0663 Å °-0.1028 Å °0.0756 Å °0.1152 Å °0.0421 Å °-0.0637 Å °0.0412 Å °0.0902 Å °0.0243 Å °
Refinement TLS groupSelection details: { A|* }

+
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://pdbjlvh1.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