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- PDB-9yv4: Crystal structure of the human DCAF1 WDR domain in complex with O... -

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Basic information

Entry
Database: PDB / ID: 9yv4
TitleCrystal structure of the human DCAF1 WDR domain in complex with OICR-41109
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / DCAF1 / SGC / Structural Genomics / 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: 1.6 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: Commun Biol / Year: 2025
Title: OICR-41103 as a chemical probe for the DCAF1 WD40 domain.
Authors: Kimani, S.W. / Noureldin, M. / Wilson, B. / Hoffer, L. / Green, S.R. / Szewczyk, M.M. / Gonzalez-Alvarez, H. / Mohammed, M. / Chan, M. / Krausser, C. / Li, A.S.M. / Hajian, T. / Tucker, S. / ...Authors: Kimani, S.W. / Noureldin, M. / Wilson, B. / Hoffer, L. / Green, S.R. / Szewczyk, M.M. / Gonzalez-Alvarez, H. / Mohammed, M. / Chan, M. / Krausser, C. / Li, A.S.M. / Hajian, T. / Tucker, S. / Joshi, D. / Saraon, P. / Theriault, B. / Kim, J.S. / Santhakumar, V. / Loppnau, P. / Li, Y. / Seitova, A. / Dong, A. / Kiyota, T. / Hammann, T. / Gehrtz, P. / Patel, B. / Rathod, V. / Vala, A. / Rout, B. / Jagodra, P. / Brown, P.J. / Aman, A. / Ramnauth, J. / Poda, G. / Uehling, D. / Arrowsmith, C.H. / Barsyte-Lovejoy, D. / Marcellus, R. / Ackloo, S. / Mamai, A. / Al-Awar, R. / Halabelian, L.
History
DepositionOct 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)72,3197
Polymers71,1862
Non-polymers1,1335
Water10,034557
1
A: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1594
Polymers35,5931
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1593
Polymers35,5931
Non-polymers5662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.009, 51.263, 79.970
Angle α, β, γ (deg.)90.00, 90.72, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 3 / Auth seq-ID: 1102 - 1107 / Label seq-ID: 27 - 32

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.998724, -0.046106, -0.020604), (-0.045579, 0.998638, -0.025388), (0.021746, -0.024417, -0.999465)1.80024, -25.33722, 40.50572

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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-A1CY9 / (4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide


Mass: 543.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H22Cl2F2N4O2 / 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-UNX / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% w/v PEG 3350, 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-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: 1.6→50 Å / Num. obs: 78143 / % possible obs: 99.7 % / Redundancy: 5.3 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.038 / Rrim(I) all: 0.088 / Χ2: 0.826 / Net I/σ(I): 7.5 / Num. measured all: 414398
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.634.70.80238810.7390.9220.4020.90.73599.5
1.63-1.665.10.70539010.8010.9430.3380.7840.73999.6
1.66-1.695.30.62738400.8550.960.2920.6930.74899.8
1.69-1.725.30.52738800.8950.9720.2470.5840.76199.4
1.72-1.764.80.4438830.9130.9770.2160.4920.76999.8
1.76-1.85.30.3938900.9430.9850.1810.4310.78999.8
1.8-1.855.40.31538630.9590.990.1460.3490.79799.8
1.85-1.95.40.26438960.9730.9930.1220.2910.81899.7
1.9-1.955.20.20838860.9740.9930.10.2320.80199.8
1.95-2.025.20.16639170.9830.9960.0790.1840.81599.8
2.02-2.095.60.1438810.990.9980.0640.1540.80899.7
2.09-2.175.30.11739150.9930.9980.0550.130.8399.8
2.17-2.275.30.09839040.9940.9980.0470.1090.87899.8
2.27-2.395.70.08738770.9960.9990.040.0960.86899.7
2.39-2.545.50.07439210.9960.9990.0350.0820.82299.6
2.54-2.745.20.06438980.9970.9990.0310.0720.88499.7
2.74-3.015.60.05639340.9960.9990.0260.0620.94699.6
3.01-3.455.30.04539520.9980.9990.0210.050.87699.9
3.45-4.345.50.0439550.9980.9990.0190.0440.88699.6
4.34-505.30.03940690.9970.9990.0190.0430.90999.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-3000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→43.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.825 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19364 1205 1.5 %RANDOM
Rwork0.17663 ---
obs0.17691 76918 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.046 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20.44 Å2
2---0.67 Å2-0 Å2
3---1.12 Å2
Refinement stepCycle: 1 / Resolution: 1.6→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4672 0 77 557 5306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125041
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164511
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.7856887
X-RAY DIFFRACTIONr_angle_other_deg0.5431.75810376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5855640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.735522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34110762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026215
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021223
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_it1.5511.642497
X-RAY DIFFRACTIONr_mcbond_other1.551.6392496
X-RAY DIFFRACTIONr_mcangle_it2.5132.9333146
X-RAY DIFFRACTIONr_mcangle_other2.5132.9343147
X-RAY DIFFRACTIONr_scbond_it2.0851.8482544
X-RAY DIFFRACTIONr_scbond_other2.0841.8482545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.323.2933738
X-RAY DIFFRACTIONr_long_range_B_refined5.30218.385510
X-RAY DIFFRACTIONr_long_range_B_other5.12717.255351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
47loose positional0.795
36tight thermal4.560.5
47loose thermal5.3410
LS refinement shellResolution: 1.6→1.641 Å
RfactorNum. reflection% reflection
Rfree0.304 74 -
Rwork0.268 5549 -
obs--98.08 %

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