[English] 日本語
Yorodumi
- PDB-8ok1: WD repeat containing protein 5 (WDR5)- N225A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ok1
TitleWD repeat containing protein 5 (WDR5)- N225A mutant
ComponentsGlutathione S-transferase class-mu 26 kDa isozyme,WD repeat-containing protein 5
KeywordsGENE REGULATION / Scaffold protein / complex component / WD40 repeat
Function / homology
Function and homology information


Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / Formation of WDR5-containing histone-modifying complexes / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Neddylation / histone H3Q5ser reader activity / histone H3K4me1 reader activity / MLL3/4 complex ...Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / Formation of WDR5-containing histone-modifying complexes / HATs acetylate histones / PKMTs methylate histone lysines / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / Neddylation / histone H3Q5ser reader activity / histone H3K4me1 reader activity / MLL3/4 complex / Set1C/COMPASS complex / ATAC complex / histone H3K4me3 reader activity / NSL complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / regulation of cell division / glutathione transferase / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / glutathione transferase activity / glutathione metabolic process / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / mitotic spindle / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
WDR5 beta-propeller domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal ...WDR5 beta-propeller domain / Glutathione S-transferase, C-terminal domain / : / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Glutathione S-transferase class-mu 26 kDa isozyme / WD repeat-containing protein 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsWolf, E. / Boergel, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: To Be Published
Title: A structural competition involving WDR5 times circadian oscillations
Authors: Wolf, E. / Boergel, A. / Rawleigh, A. / Conrady, M. / Hof, F. / Ricci, K. / Brown, S.
History
DepositionMar 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat-containing protein 5


Theoretical massNumber of molelcules
Total (without water)62,6311
Polymers62,6311
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11770 Å2
Unit cell
Length a, b, c (Å)78.498, 98.134, 80.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

-
Components

#1: Protein Glutathione S-transferase class-mu 26 kDa isozyme,WD repeat-containing protein 5 / GST 26 / Sj26 antigen / SjGST / BMP2-induced 3-kb gene protein / WD repeat-containing protein BIG-3


Mass: 62630.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wdr5, Big, Big3 / Production host: Escherichia coli (E. coli)
References: UniProt: P08515, UniProt: P61965, glutathione transferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5, 50 mM ammonium sulfate, 24% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.38→48.67 Å / Num. obs: 63526 / % possible obs: 99.3 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Net I/σ(I): 13
Reflection shellResolution: 1.38→1.4 Å / Num. unique obs: 2949 / CC1/2: 0.573

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→48.67 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.254 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21774 3050 4.8 %RANDOM
Rwork0.19437 ---
obs0.19549 60006 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.859 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.38→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 245 2572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172249
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.6223273
X-RAY DIFFRACTIONr_angle_other_deg1.4811.5865215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.635305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33924.89494
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55215409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.83152
X-RAY DIFFRACTIONr_chiral_restr0.090.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022707
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02525
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5571.6471217
X-RAY DIFFRACTIONr_mcbond_other1.5441.6441216
X-RAY DIFFRACTIONr_mcangle_it2.2062.4661523
X-RAY DIFFRACTIONr_mcangle_other2.212.4691524
X-RAY DIFFRACTIONr_scbond_it2.5681.921191
X-RAY DIFFRACTIONr_scbond_other2.5671.9221192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9272.7581751
X-RAY DIFFRACTIONr_long_range_B_refined5.43920.4672679
X-RAY DIFFRACTIONr_long_range_B_other5.3720.0012632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.381→1.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree1.164 219 -
Rwork1.254 4143 -
obs--94.35 %

+
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