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- PDB-9ydg: Crystal structure of the human DCAF1 WDR domain in complex with O... -

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Basic information

Entry
Database: PDB / ID: 9ydg
TitleCrystal structure of the human DCAF1 WDR domain in complex with OICR-41074
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / DCAF1 / SGC / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium
Function / homology
Function and homology information


cell competition in a multicellular organism / histone H2AT120 kinase activity / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / post-translational protein modification / B cell differentiation / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process ...cell competition in a multicellular organism / histone H2AT120 kinase activity / V(D)J recombination / Cul4-RING E3 ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / post-translational protein modification / B cell differentiation / nuclear estrogen receptor binding / fibrillar center / positive regulation of protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein ubiquitination / protein serine kinase activity / centrosome / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
Authorskimani, S. / Dong, A. / Li, Y. / Seitova, A. / Mamai, A. / Al-awar, R. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074
Authors: kimani, S. / Dong, A. / Li, Y. / Seitova, A. / Mamai, A. / Al-awar, R. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionSep 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DDB1- and CUL4-associated factor 1
B: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4497
Polymers71,1862
Non-polymers1,2635
Water7,152397
1
A: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2164
Polymers35,5931
Non-polymers6233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2323
Polymers35,5931
Non-polymers6392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.067, 87.819, 73.680
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 35592.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1CU7 / (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-(morpholin-4-yl)-3-oxoprop-1-en-1-yl]-1H-pyrrole-3-carboxamide


Mass: 577.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H24Cl2F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350, 0.2 M Potassium Fluoride

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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: 1.54→50 Å / Num. obs: 89670 / % possible obs: 98.4 % / Redundancy: 6.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Χ2: 0.704 / Net I/σ(I): 7.9 / Num. measured all: 565879
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.54-1.574.90.60237800.8430.9560.2820.6680.71383.3
1.57-1.65.20.57341310.8650.9630.260.6320.72591
1.6-1.635.50.56743800.8840.9690.2570.6250.71196.3
1.63-1.665.90.53544640.9050.9750.2360.5860.71799.1
1.66-1.696.50.48145370.9370.9840.2030.5230.71199.8
1.69-1.736.40.39445240.9580.9890.1660.4280.73999.8
1.73-1.786.10.31945270.9660.9910.1390.3490.73999.7
1.78-1.836.50.27145540.9740.9930.1140.2940.74599.8
1.83-1.886.50.20945370.9840.9960.0880.2270.76599.8
1.88-1.946.10.16245370.990.9970.070.1770.76999.8
1.94-2.016.60.13345480.9920.9980.0550.1440.776100
2.01-2.096.60.10645520.9950.9990.0440.1150.738100
2.09-2.196.30.08545390.9960.9990.0370.0930.73699.9
2.19-2.36.80.0745520.9970.9990.0290.0760.709100
2.3-2.446.50.06145620.9980.9990.0260.0660.67399.9
2.44-2.636.80.05245510.99810.0210.0560.631100
2.63-2.96.70.04445630.99910.0180.0480.589100
2.9-3.326.60.03545740.99910.0150.0380.54499.9
3.32-4.186.60.0345920.99910.0130.0330.4899.9
4.18-506.60.02946660.99910.0120.0310.896100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
REFMACphasing
PDB_EXTRACTdata extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→48.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.992 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21788 4383 4.9 %RANDOM
Rwork0.18813 ---
obs0.1896 85255 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å2-1.53 Å2
2---0.4 Å2-0 Å2
3----1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.54→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 84 397 5098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124976
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164377
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.7826798
X-RAY DIFFRACTIONr_angle_other_deg0.5461.75610059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5955628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.018520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28910732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021207
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_it2.112.2952465
X-RAY DIFFRACTIONr_mcbond_other2.112.2962466
X-RAY DIFFRACTIONr_mcangle_it3.3254.1053102
X-RAY DIFFRACTIONr_mcangle_other3.3254.1053103
X-RAY DIFFRACTIONr_scbond_it2.6222.5462511
X-RAY DIFFRACTIONr_scbond_other2.6222.5472512
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1434.5493695
X-RAY DIFFRACTIONr_long_range_B_refined5.84725.345266
X-RAY DIFFRACTIONr_long_range_B_other5.78423.965178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 277 -
Rwork0.299 5280 -
obs--82.69 %

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