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

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Basic information

Entry
Database: PDB / ID: 9ply
TitleCrystal structure of the human DCAF1 WDR domain in complex with OICR-40156
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE
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: 1.4 Å
AuthorsKimani, S. / Dong, A. / Li, Y. / Seitova, A. / Krausser, C. / Wilson, B. / Al-awar, R. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. ...Kimani, S. / Dong, A. / Li, Y. / Seitova, A. / Krausser, C. / Wilson, B. / 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-40156
Authors: Kimani, S. / Dong, A. / Li, Y. / Seitova, A. / Krausser, C. / Wilson, B. / Al-awar, R. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionJul 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)72,4698
Polymers71,1862
Non-polymers1,2836
Water10,124562
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.350, 88.600, 73.409
Angle α, β, γ (deg.)90.00, 98.01, 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-A1CI0 / (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(3-methoxypropyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide


Mass: 579.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H26Cl2F2N4O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95369 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: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 121825 / % possible obs: 99.4 % / Redundancy: 6.6 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Χ2: 0.84 / Net I/σ(I): 8.6 / Num. measured all: 801001
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.4-1.424.90.67557220.8040.9440.3230.7520.59393.3
1.42-1.455.70.61860280.8640.9630.2730.6770.59898.4
1.45-1.486.30.56160060.8960.9720.2380.6110.61499.2
1.48-1.516.70.48360600.9320.9820.1980.5220.61899.5
1.51-1.546.90.41561270.9530.9880.1690.4490.63999.5
1.54-1.586.90.34260400.9650.9910.1390.370.64999.7
1.58-1.626.90.29361130.9710.9930.120.3170.6699.8
1.62-1.666.80.24861290.9780.9940.1020.2680.67799.8
1.66-1.716.60.20160730.9830.9960.0840.2190.70299.9
1.71-1.766.30.16561170.9870.9970.0710.180.71499.9
1.76-1.836.60.13761300.990.9980.0570.1480.744100
1.83-1.96.60.11161070.9930.9980.0470.1210.795100
1.9-1.996.70.0961320.9950.9990.0370.0980.837100
1.99-2.097.20.07860910.9960.9990.0310.0840.885100
2.09-2.227.10.06861450.9970.9990.0270.0730.951100
2.22-2.3970.06161370.9970.9990.0250.0661.013100
2.39-2.636.90.05661280.9980.9990.0230.0611.078100
2.63-3.026.40.04961540.9980.9990.0210.0531.197100
3.02-3.86.10.04361680.9980.9990.0190.0471.35699.8
3.8-506.90.04262180.9980.9990.0170.0461.33299.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
HKL-3000data reduction
REFMACphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→44.34 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.94 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17423 5964 4.9 %RANDOM
Rwork0.14583 ---
obs0.14724 115828 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å2-0.41 Å2
2--0.09 Å20 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.4→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4701 0 2 562 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124962
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164423
X-RAY DIFFRACTIONr_angle_refined_deg1.1351.7876771
X-RAY DIFFRACTIONr_angle_other_deg0.4391.75910155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7495623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38810752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021211
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_it3.2121.5992445
X-RAY DIFFRACTIONr_mcbond_other3.2121.62446
X-RAY DIFFRACTIONr_mcangle_it5.1942.8643074
X-RAY DIFFRACTIONr_mcangle_other5.1942.8643075
X-RAY DIFFRACTIONr_scbond_it3.6371.7832517
X-RAY DIFFRACTIONr_scbond_other3.6371.7842518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.683.1813695
X-RAY DIFFRACTIONr_long_range_B_refined11.70819.945448
X-RAY DIFFRACTIONr_long_range_B_other10.3816.935270
X-RAY DIFFRACTIONr_rigid_bond_restr2.09539385
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 428 -
Rwork0.228 8096 -
obs--94.45 %

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