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- PDB-8t5i: Crystal structure of human WDR5 in complex with MR4397 -

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Basic information

Entry
Database: PDB / ID: 8t5i
TitleCrystal structure of human WDR5 in complex with MR4397
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION / WD-repeat / WDR / WDR5 / SGC
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
G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-ZHF / 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. / Li, F. / Loppnau, P. / Ackloo, S. / Vedadi, M. / Brown, P.J. / 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 human WDR5 in complex with MR4397
Authors: Kimani, S. / Dong, A. / Li, F. / Loppnau, P. / Ackloo, S. / Vedadi, M. / Brown, P.J. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)70,13416
Polymers68,5802
Non-polymers1,55414
Water7,855436
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8996
Polymers34,2901
Non-polymers6095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,23510
Polymers34,2901
Non-polymers9459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.382, 86.370, 80.796
Angle α, β, γ (deg.)90.00, 96.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964

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Non-polymers , 5 types, 450 molecules

#2: Chemical ChemComp-ZHF / N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[(1H-imidazol-1-yl)methyl]benzamide


Mass: 422.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26N4O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% PEG3350, 0.2 M (NH4)2SO4, 0.1M BTP pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 72369 / % possible obs: 95.9 % / Redundancy: 5.7 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.062 / Rrim(I) all: 0.149 / Χ2: 1.332 / Net I/σ(I): 7.7 / Num. measured all: 416078
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.735.40.98235480.6580.8910.4561.0870.7195.1
1.73-1.765.50.89436000.7110.9120.4150.9890.74695
1.76-1.795.40.76635980.7450.9240.3620.8510.75395.1
1.79-1.835.10.62134890.8080.9450.2990.6930.81893.4
1.83-1.875.30.52733580.8250.9510.250.5860.86889.5
1.87-1.915.80.45936220.8730.9650.2090.5060.89896.6
1.91-1.9660.436800.9010.9740.1820.4410.91396.3
1.96-2.0260.34336220.9190.9790.1560.3780.98696.9
2.02-2.0760.31636370.940.9840.1450.3491.11996.6
2.07-2.1460.26736300.9490.9870.1230.2951.19397.2
2.14-2.225.90.23836990.9550.9880.110.2631.31997.1
2.22-2.315.80.21736300.9620.990.1010.241.39397.1
2.31-2.415.70.18636440.9580.9890.0870.2061.40297
2.41-2.545.50.16136310.9730.9930.0760.1781.51395.7
2.54-2.75.40.1434380.9720.9930.0670.1561.7791.4
2.7-2.916.20.12737030.9810.9950.0570.141.90997.9
2.91-3.26.10.10337300.9840.9960.0470.1141.98198.7
3.2-3.6660.09237530.9880.9970.0410.1012.34198.4
3.66-4.615.70.07536960.9920.9980.0340.0831.9897.6
4.61-5060.06536610.9930.9980.0290.0711.62394.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→49.06 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.295 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23174 1467 2 %RANDOM
Rwork0.19654 ---
obs0.19722 70899 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.577 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.08 Å2
2--0.37 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4668 0 108 436 5212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134957
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174488
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.6216737
X-RAY DIFFRACTIONr_angle_other_deg1.3061.59210471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6515630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12824.974191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.556156
X-RAY DIFFRACTIONr_chiral_restr0.0660.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02985
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_it1.0961.7562471
X-RAY DIFFRACTIONr_mcbond_other1.0941.7552469
X-RAY DIFFRACTIONr_mcangle_it1.7012.6273097
X-RAY DIFFRACTIONr_mcangle_other1.72.6273098
X-RAY DIFFRACTIONr_scbond_it1.4781.9462484
X-RAY DIFFRACTIONr_scbond_other1.4781.9472485
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.292.8443633
X-RAY DIFFRACTIONr_long_range_B_refined4.15721.5155473
X-RAY DIFFRACTIONr_long_range_B_other3.98921.0665357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 132 -
Rwork0.268 5034 -
obs--92.5 %

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