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- PDB-9d5z: Crystal structure of the human WDR5 in complex with LH168 compound -

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Basic information

Entry
Database: PDB / ID: 9d5z
TitleCrystal structure of the human WDR5 in complex with LH168 compound
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION / WD-repeat / WDR / WDR5 / SGC
Function / homology
Function and homology information


Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex ...Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / : / positive regulation of gluconeogenesis / 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 / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / regulation of cell cycle / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
WD domain, G-beta repeat / 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
: / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKimani, S. / Dong, A. / Hoffmann, L. / Nemec, V. / Ackloo, S. / Muller-Knapp, S. / Knapp, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of the human WDR5 in complex with LH168 compound
Authors: Kimani, S. / Dong, A. / Hoffmann, L. / Nemec, V. / Ackloo, S. / Muller-Knapp, S. / Knapp, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionAug 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)70,0599
Polymers68,5802
Non-polymers1,4807
Water8,539474
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9994
Polymers34,2901
Non-polymers7093
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0615
Polymers34,2901
Non-polymers7714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.951, 61.185, 64.605
Angle α, β, γ (deg.)110.41, 91.22, 112.20
Int Tables number1
Space group name H-MP1

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Components

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Chemical ChemComp-A1A16 / (3P)-N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-5-[(1H-imidazol-1-yl)methyl]benzamide


Mass: 584.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31F3N6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M Ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18049 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18049 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 63599 / % possible obs: 94.1 % / Redundancy: 3.4 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Χ2: 1.225 / Net I/σ(I): 8.3 / Num. measured all: 218124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.733.20.31626810.9360.9830.20.3760.780.6
1.73-1.763.20.2828980.950.9870.1820.3360.71385
1.76-1.793.30.24330890.9650.9910.1540.2890.71590.3
1.79-1.833.50.23630570.9730.9930.1470.2790.72192.9
1.83-1.873.50.19632170.9790.9950.1220.2320.72193.7
1.87-1.913.30.15531720.9860.9970.0990.1850.72294
1.91-1.963.40.13331820.9880.9970.0850.1590.7494.1
1.96-2.023.50.11631980.9920.9980.0710.1370.73995
2.02-2.073.40.10431790.9920.9980.0660.1240.78594.4
2.07-2.143.40.09332210.9930.9980.060.1110.8394.3
2.14-2.223.60.07931850.9950.9990.0480.0930.73894.9
2.22-2.313.60.07632520.9950.9990.0470.090.76995.7
2.31-2.413.30.06632160.9940.9980.0440.081.16696.3
2.41-2.543.60.05732870.9960.9990.0350.0670.96996.5
2.54-2.73.40.04832640.9960.9990.0310.0571.29496.8
2.7-2.913.60.0432920.9970.9990.0250.0471.28896.8
2.91-3.23.50.03532740.9980.9990.0220.0410.99497.3
3.2-3.663.40.02832980.99810.0170.0330.75897.5
3.66-4.613.50.02633060.9970.9990.0160.0312.54497.8
4.61-503.50.03133310.9960.9990.020.0366.02998.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.89 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.53 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18872 1212 1.9 %RANDOM
Rwork0.1394 ---
obs0.14033 62385 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.816 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0.25 Å2-0.91 Å2
2--1.88 Å20.31 Å2
3----1.67 Å2
Refinement stepCycle: 1 / Resolution: 1.7→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 0 474 5185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124919
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164499
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.7766702
X-RAY DIFFRACTIONr_angle_other_deg0.4751.76910404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3535622
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.24158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54110761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021084
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_it4.282.422461
X-RAY DIFFRACTIONr_mcbond_other4.2722.422461
X-RAY DIFFRACTIONr_mcangle_it6.5274.343086
X-RAY DIFFRACTIONr_mcangle_other6.5274.3413087
X-RAY DIFFRACTIONr_scbond_it4.5892.5962458
X-RAY DIFFRACTIONr_scbond_other4.5892.5982459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9214.6963615
X-RAY DIFFRACTIONr_long_range_B_refined12.64925.575356
X-RAY DIFFRACTIONr_long_range_B_other11.38123.135233
X-RAY DIFFRACTIONr_rigid_bond_restr2.2439418
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.743 Å
RfactorNum. reflection% reflection
Rfree0.24 85 -
Rwork0.203 3885 -
obs--79.16 %

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