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- PDB-4ql1: Crystal structure of human WDR5 in complex with compound OICR-9429 -

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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 / histone methyltransferase complex / regulation of tubulin deacetylation / 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 / histone methyltransferase complex / regulation of tubulin deacetylation / 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 / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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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.

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Experimental details

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Experiment

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

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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

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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

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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 %

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