[English] 日本語
Yorodumi
- PDB-6v3x: Crystal structure of EED in complex with PALI1-K1241me3 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v3x
TitleCrystal structure of EED in complex with PALI1-K1241me3 peptide
Components
  • PALI1 peptide
  • Polycomb protein EED
KeywordsGENE REGULATION / EED / PALI1 / LCOR / C10ORF12 / tri-methyl-lysine
Function / homology
Function and homology information


ESC/E(Z) complex / spinal cord development / Transcriptional Regulation by E2F6 / enzyme activator activity / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / transcription corepressor binding / Defective pyroptosis / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis ...ESC/E(Z) complex / spinal cord development / Transcriptional Regulation by E2F6 / enzyme activator activity / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / transcription corepressor binding / Defective pyroptosis / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / heterochromatin formation / 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. / 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
Polycomb protein EED
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, Q. / Davidovich, C.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE180100219 Australia
Australian Research Council (ARC)DP190103407 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1162921 Australia
Citation
Journal: Nat Commun / Year: 2021
Title: PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis.
Authors: Zhang, Q. / Agius, S.C. / Flanigan, S.F. / Uckelmann, M. / Levina, V. / Owen, B.M. / Davidovich, C.
#1: Journal: Nat Commun / Year: 2021
Title: PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis
Authors: Zhang, Q. / Aguis, S.C. / Flanigan, S.F. / Uckelmann, M. / Levina, V. / Owen, B.M. / Davidovich, C.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 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_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polycomb protein EED
B: PALI1 peptide


Theoretical massNumber of molelcules
Total (without water)43,0892
Polymers43,0892
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-5 kcal/mol
Surface area14750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.243, 84.721, 90.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
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: 42356.246 Da / Num. of mol.: 1 / Fragment: UNP residues 81-440
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: Protein/peptide PALI1 peptide


Mass: 732.953 Da / Num. of mol.: 1 / Fragment: residues 1239-1244 / Source method: obtained synthetically / Details: UNP Q96JN0-3 / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.6 M sodium formate, 10 mM TCEP, 5% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.7→47.76 Å / Num. obs: 47118 / % possible obs: 97.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 20.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.025 / Rrim(I) all: 0.071 / Net I/σ(I): 16.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 8 % / Rmerge(I) obs: 0.631 / Num. unique obs: 6664 / CC1/2: 0.898 / Rpim(I) all: 0.234 / Rrim(I) all: 0.674 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
REFMAC5.5refinement
PHENIX1.17.1_3660refinement
XDSdata processing
SCALAdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IIW

3iiw


Resolution: 1.7→35.24 Å / SU ML: 0.1323 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1999 2291 4.87 %
Rwork0.1737 44749 -
obs0.175 47040 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2863 0 0 178 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582965
X-RAY DIFFRACTIONf_angle_d0.83814036
X-RAY DIFFRACTIONf_chiral_restr0.0599439
X-RAY DIFFRACTIONf_plane_restr0.005518
X-RAY DIFFRACTIONf_dihedral_angle_d14.2308400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25671500.22182682X-RAY DIFFRACTION96.23
1.74-1.780.22521380.20232721X-RAY DIFFRACTION96.1
1.78-1.820.26971560.19362734X-RAY DIFFRACTION96.59
1.82-1.870.22311480.18662719X-RAY DIFFRACTION96.6
1.87-1.930.22771330.19222749X-RAY DIFFRACTION96.65
1.93-1.990.19561400.17282727X-RAY DIFFRACTION96.92
1.99-2.060.20571310.17362797X-RAY DIFFRACTION97.31
2.06-2.140.16681460.16252757X-RAY DIFFRACTION97.38
2.14-2.240.20571320.16472782X-RAY DIFFRACTION97.43
2.24-2.360.21881490.18372808X-RAY DIFFRACTION97.75
2.36-2.50.24441510.18412798X-RAY DIFFRACTION98.53
2.5-2.70.2171350.19292822X-RAY DIFFRACTION97.72
2.7-2.970.24881170.19962865X-RAY DIFFRACTION98.45
2.97-3.40.19611400.17812877X-RAY DIFFRACTION98.89
3.4-4.280.18541280.15242943X-RAY DIFFRACTION99
4.28-35.240.16311970.15652968X-RAY DIFFRACTION98.26

+
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