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- PDB-9bhs: Crystal structure of the WDR domain of human DCAF1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9bhs
TitleCrystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE / 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
: / Unknown ligand / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.43 Å
Authorskimani, S. / Dong, A. / Li, Y. / Seitova, A. / Al-Awar, R. / Wilson, B. / 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 WDR domain of human DCAF1 in complex with OICR-9939 compound
Authors: kimani, S. / Dong, A. / Li, Y. / Seitova, A. / Al-Awar, R. / Wilson, B. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionApr 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: 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)72,3139
Polymers71,1862
Non-polymers1,1277
Water8,935496
1
A: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1293
Polymers35,5931
Non-polymers5362
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)36,1836
Polymers35,5931
Non-polymers5905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.442, 87.884, 73.075
Angle α, β, γ (deg.)90.00, 96.75, 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-A1APJ / (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(1-methyl-1H-pyrazol-4-yl)-1H-pyrrole-3-carboxamide


Mass: 518.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H19Cl2F2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 108966 / % possible obs: 97.3 % / Redundancy: 6.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Χ2: 0.734 / Net I/σ(I): 8.9 / Num. measured all: 721964
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.43-1.455.50.46345420.8980.9730.210.5110.5181.7
1.45-1.486.20.41452060.9340.9830.1790.4520.52193.9
1.48-1.516.70.36155660.9580.9890.150.3920.52599.3
1.51-1.546.70.30255170.9680.9920.1250.3280.55499
1.54-1.576.70.24755050.9790.9950.1030.2680.5798.7
1.57-1.616.60.21555120.9820.9950.090.2340.56298.5
1.61-1.656.40.18453970.9850.9960.0780.2010.56897
1.65-1.76.40.15453560.9880.9970.0650.1670.58196.2
1.7-1.756.80.13455930.9920.9980.0550.1450.60699.5
1.75-1.86.80.11355450.9940.9980.0460.1220.62999.2
1.8-1.876.70.09455220.9950.9990.0390.1020.66498.7
1.87-1.946.60.07754630.9960.9990.0320.0840.72497.8
1.94-2.036.30.06553630.9970.9990.0280.0710.80596.1
2.03-2.146.90.0655590.9970.9990.0250.0650.89799.4
2.14-2.276.90.05155540.9980.9990.0210.0560.90999.3
2.27-2.456.80.04655560.99810.0190.0490.89198.6
2.45-2.696.60.04154560.99910.0170.0450.92797.2
2.69-3.087.10.03755850.99910.0150.041.0499.4
3.08-3.886.60.03155150.99910.0130.0331.08997.7
3.88-506.90.02756540.99910.0110.0290.94398.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data processing
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.43→42.5 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.064 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16957 5396 5 %RANDOM
Rwork0.1405 ---
obs0.14194 103543 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.638 Å2
Baniso -1Baniso -2Baniso -3
1-1.86 Å2-0 Å2-0.53 Å2
2---1.11 Å20 Å2
3----0.61 Å2
Refinement stepCycle: 1 / Resolution: 1.43→42.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 75 496 5269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125183
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164584
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.7877101
X-RAY DIFFRACTIONr_angle_other_deg0.5061.7610533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5475659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.77527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06210775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026531
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021291
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_it3.3491.6962549
X-RAY DIFFRACTIONr_mcbond_other3.3431.6952548
X-RAY DIFFRACTIONr_mcangle_it5.3193.0433228
X-RAY DIFFRACTIONr_mcangle_other5.323.0433229
X-RAY DIFFRACTIONr_scbond_it3.8551.8822634
X-RAY DIFFRACTIONr_scbond_other3.8541.8822634
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9323.3663871
X-RAY DIFFRACTIONr_long_range_B_refined11.07119.725466
X-RAY DIFFRACTIONr_long_range_B_other10.07817.565330
X-RAY DIFFRACTIONr_rigid_bond_restr2.08539767
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.466 Å
RfactorNum. reflection% reflection
Rfree0.21 361 -
Rwork0.195 6452 -
obs--82.43 %

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