[English] 日本語
Yorodumi
- PDB-4ql1: Crystal structure of human WDR5 in complex with compound OICR-9429 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ql1
TitleCrystal structure of human WDR5 in complex with compound OICR-9429
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION/INHIBITOR / WDR5 / WD repeat domain 5 / OICR-9429 inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / RMTs methylate histone arginines / mitotic spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / WD domain, G-beta repeat / WD40 repeats ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / 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-35Q / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDong, A. / Dombrovski, L. / Walker, J.R. / Getlik, M. / Kuznetsova, E. / Smil, D. / Barsyte, D. / Li, F. / Poda, G. / Senisterra, G. ...Dong, A. / Dombrovski, L. / Walker, J.R. / Getlik, M. / Kuznetsova, E. / Smil, D. / Barsyte, D. / Li, F. / Poda, G. / Senisterra, G. / Marcellus, R. / Al-Awar, R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Schapira, M. / Vedadi, M. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Pharmacological targeting of the Wdr5-MLL interaction in C/EBP alpha N-terminal leukemia.
Authors: Grebien, F. / Vedadi, M. / Getlik, M. / Giambruno, R. / Grover, A. / Avellino, R. / Skucha, A. / Vittori, S. / Kuznetsova, E. / Smil, D. / Barsyte-Lovejoy, D. / Li, F. / Poda, G. / Schapira, ...Authors: Grebien, F. / Vedadi, M. / Getlik, M. / Giambruno, R. / Grover, A. / Avellino, R. / Skucha, A. / Vittori, S. / Kuznetsova, E. / Smil, D. / Barsyte-Lovejoy, D. / Li, F. / Poda, G. / Schapira, M. / Wu, H. / Dong, A. / Senisterra, G. / Stukalov, A. / Huber, K.V. / Schonegger, A. / Marcellus, R. / Bilban, M. / Bock, C. / Brown, P.J. / Zuber, J. / Bennett, K.L. / Al-Awar, R. / Delwel, R. / Nerlov, C. / Arrowsmith, C.H. / Superti-Furga, G.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Non-polymer description
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Jul 29, 2015Group: Database references
Revision 1.4Feb 24, 2016Group: Database references
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8458
Polymers68,5802
Non-polymers1,2656
Water5,873326
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8453
Polymers34,2901
Non-polymers5562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0005
Polymers34,2901
Non-polymers7104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.843, 56.628, 64.688
Angle α, β, γ (deg.)71.450, 88.940, 65.430
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34289.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2RpRARE / References: UniProt: P61964

-
Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-35Q / N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide


Mass: 555.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H32F3N5O3
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsAUTHORS STATE THAT DUE TO POOR ELECTRON DENSITY, COORDINATES FOR THE MORPHOLINO GROUP OF OICR-9429 ...AUTHORS STATE THAT DUE TO POOR ELECTRON DENSITY, COORDINATES FOR THE MORPHOLINO GROUP OF OICR-9429 HAVE BEEN OMITTED FROM THE MODEL.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.2 M NH4oAC, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 85828 / % possible obs: 94.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.067 / Χ2: 2.952 / Net I/σ(I): 39.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.533.70.39232021.355170.2
1.53-1.553.70.33539271.449187.4
1.55-1.583.90.30442751.515194.7
1.58-1.623.90.26343741.656195.1
1.62-1.653.90.22642521.792195.5
1.65-1.693.90.243221.881195.5
1.69-1.733.90.17443452.078195.6
1.73-1.783.90.15443362.271195.9
1.78-1.833.90.13243572.52196.2
1.83-1.893.90.1143812.956196.2
1.89-1.963.80.09743573.426196.6
1.96-2.043.70.08543623.67196.8
2.04-2.133.70.07744063.814196.9
2.13-2.243.70.07144223.955197.2
2.24-2.383.60.06943724.1197.4
2.38-2.563.60.06544634.203197.7
2.56-2.823.50.05744304.214198.1
2.82-3.233.50.05344444.354198.4
3.23-4.073.50.04644493.986198.3
4.07-503.50.04743524.118196

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR4

3ur4


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.618 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 1695 2 %RANDOM
Rwork0.1954 ---
obs0.196 85825 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.5 Å2 / Biso mean: 15.328 Å2 / Biso min: 6.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0.12 Å2-0.2 Å2
2--0.41 Å20.01 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 84 326 5030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024911
X-RAY DIFFRACTIONr_bond_other_d0.0020.024540
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9536707
X-RAY DIFFRACTIONr_angle_other_deg0.8263.00510492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.79825.109184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08715796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.038157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025559
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021108
X-RAY DIFFRACTIONr_mcbond_it0.8581.4692457
X-RAY DIFFRACTIONr_mcbond_other0.8581.4692456
X-RAY DIFFRACTIONr_mcangle_it1.4452.1983076
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 106 -
Rwork0.23 4578 -
all-4684 -
obs--69.61 %

+
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