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- PDB-9y4q: Crystal structure of the human DCAF1 WDR domain in complex with O... -

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Basic information

Entry
Database: PDB / ID: 9y4q
TitleCrystal structure of the human DCAF1 WDR domain in complex with OICR-40102
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / DCAF1 / SGC
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 / FOURIER SYNTHESIS / Resolution: 1.48 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 support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102
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 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: 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)72,2194
Polymers71,1862
Non-polymers1,0332
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.692, 88.192, 73.099
Angle α, β, γ (deg.)90.00, 97.47, 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-A1CR9 / (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(pyrimidin-5-yl)-1H-pyrrole-3-carboxamide


Mass: 516.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H17Cl2F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 3.2 M NaCl, 0.1 M Bis-Tris Propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 103575 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.027 / Rrim(I) all: 0.064 / Χ2: 0.867 / Net I/σ(I): 10.1 / Num. measured all: 574878
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.48-1.515.30.79451630.7180.9140.380.8830.73699.9
1.51-1.535.60.69252160.7850.9380.3210.7650.728100
1.53-1.565.70.56951150.840.9560.2610.6280.742100
1.56-1.595.60.4851390.8710.9650.2210.530.764100
1.59-1.635.60.42551750.8950.9720.1950.4690.771100
1.63-1.675.50.34951460.9170.9780.1620.3860.769100
1.67-1.715.30.28751750.9430.9850.1360.3190.807100
1.71-1.755.10.23751660.9570.9890.1150.2640.82599.7
1.75-1.815.50.19652020.9720.9930.0910.2160.825100
1.81-1.865.40.15551000.9780.9940.0740.1730.845100
1.86-1.935.40.12251930.9860.9970.0580.1360.879100
1.93-2.015.90.09651680.9920.9980.0430.1060.883100
2.01-2.15.90.08151910.9940.9980.0370.0890.918100
2.1-2.215.90.06951770.9950.9990.0310.0760.94100
2.21-2.355.80.05852000.9970.9990.0260.0640.956100
2.35-2.535.70.05451950.9970.9990.0250.0590.999100
2.53-2.795.50.04751620.9970.9990.0220.0520.99299.9
2.79-3.1950.03952110.9980.9990.0190.0431.00999.9
3.19-4.025.20.03352070.99910.0160.0371.01399.7
4.02-505.90.03252740.99910.0140.0350.93199.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
REFMACphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.48→38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.732 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19321 5152 5 %RANDOM
Rwork0.15779 ---
obs0.15955 98392 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20.02 Å2
2---1 Å2-0 Å2
3---0.94 Å2
Refinement stepCycle: 1 / Resolution: 1.48→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 70 455 5179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124975
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164422
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.7846791
X-RAY DIFFRACTIONr_angle_other_deg0.5111.75310152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5465624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.69524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11610748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2752
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
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_it3.6341.7842446
X-RAY DIFFRACTIONr_mcbond_other3.6341.7842447
X-RAY DIFFRACTIONr_mcangle_it5.6613.1923071
X-RAY DIFFRACTIONr_mcangle_other5.663.1933072
X-RAY DIFFRACTIONr_scbond_it4.0882.0012529
X-RAY DIFFRACTIONr_scbond_other4.0872.0012530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2663.5823716
X-RAY DIFFRACTIONr_long_range_B_refined11.4320.735368
X-RAY DIFFRACTIONr_long_range_B_other10.44118.545263
X-RAY DIFFRACTIONr_rigid_bond_restr2.2339397
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.504 Å
RfactorNum. reflection% reflection
Rfree0.274 357 -
Rwork0.248 6234 -
obs--85.4 %

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