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- PDB-5eal: Crystal structure of human WDR5 in complex with compound 9h -

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Basic information

Entry
Database: PDB / ID: 5eal
TitleCrystal structure of human WDR5 in complex with compound 9h
ComponentsWD repeat-containing protein 5
KeywordsTranscription/Transcription inhibitor / WDR5 / compound 9h / Structural Genomics / Structural Genomics Consortium / SGC / Transcription-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 / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / 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-5ML / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDONG, A. / DOMBROVSKI, L. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. ...DONG, A. / DOMBROVSKI, L. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. / VEDADI, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human WDR5 in complex with compound 9h
Authors: DOMBROVSKI, L. / DONG, A. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. / VEDADI, M. / Bountra, C. / Edwards, A.M. / ...Authors: DOMBROVSKI, L. / DONG, A. / SMIL, D. / GETLIK, M. / BOLSHAN, Y. / WALKER, J.R. / SENISTERRA, G. / PODA, G. / AL-AWAR, R. / SCHAPIRA, M. / VEDADI, M. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
History
DepositionOct 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)70,63647
Polymers68,5802
Non-polymers2,05645
Water8,665481
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,35125
Polymers34,2901
Non-polymers1,06124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,28522
Polymers34,2901
Non-polymers99521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.191, 60.962, 64.126
Angle α, β, γ (deg.)110.670, 90.430, 109.470
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 / Fragment: UNP residues 23-334
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 , 6 types, 526 molecules

#2: Chemical ChemComp-5ML / 3-methyl-~{N}-[2-(4-methylpiperazin-1-yl)-5-quinolin-3-yl-phenyl]benzamide


Mass: 436.548 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H28N4O
#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 24 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 5K MME, 0.1 M BisTris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 54564 / % possible obs: 94.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.071 / Χ2: 1.113 / Net I/av σ(I): 20.207 / Net I/σ(I): 9.5 / Num. measured all: 215444
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.8340.61826350.90390.5
1.83-1.8640.5226090.95390.5
1.86-1.940.41526310.97290.8
1.9-1.9440.34726641.05591.7
1.94-1.9840.29426801.04392
1.98-2.0340.25326381.03791.9
2.03-2.0840.22126701.12392.4
2.08-2.1340.19127241.06393
2.13-2.240.16526931.07593.4
2.2-2.2740.16627211.24493.8
2.27-2.353.90.14327581.09994.2
2.35-2.4440.12727171.09394.4
2.44-2.5540.11327411.17594.9
2.55-2.6940.08827521.13495.6
2.69-2.863.90.07227861.11595.9
2.86-3.083.90.05827811.19996.5
3.08-3.393.90.04328371.24197
3.39-3.883.90.03528041.23297.6
3.88-4.883.90.0328541.22798.3
4.88-503.90.03128691.23199.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UR4

3ur4


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.1949 / WRfactor Rwork: 0.1635 / FOM work R set: 0.8517 / SU B: 2.933 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1353 / SU Rfree: 0.1235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 1125 2.1 %RANDOM
Rwork0.1785 ---
obs0.1792 53391 94.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.73 Å2 / Biso mean: 23.039 Å2 / Biso min: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20.72 Å20.14 Å2
2--1.06 Å20.16 Å2
3----1.46 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 165 488 5319
Biso mean--26.12 33.18 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194989
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9316764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3675627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44225.161186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81915813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.181157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213885
X-RAY DIFFRACTIONr_mcbond_it1.0822.1512474
X-RAY DIFFRACTIONr_mcangle_it1.6723.2173099
X-RAY DIFFRACTIONr_scbond_it1.2372.2632515
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 76 -
Rwork0.29 3803 -
all-3879 -
obs--90.27 %

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