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- PDB-9d4e: Crystal structure of the human DCAF1 WDR domain in complex with O... -

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Basic information

Entry
Database: PDB / ID: 9d4e
TitleCrystal structure of the human DCAF1 WDR domain in complex with OICR-41103
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
: / CITRIC ACID / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsKimani, S. / Dong, A. / Li, Y. / Seitova, A. / Al-awar, R. / Mamai, A. / 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-1103
Authors: Kimani, S. / Dong, A. / Li, Y. / Seitova, A. / Al-awar, R. / Mamai, A. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionAug 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 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)72,5295
Polymers71,1862
Non-polymers1,3433
Water5,459303
1
A: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3613
Polymers35,5931
Non-polymers7682
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)36,1682
Polymers35,5931
Non-polymers5751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.574, 87.975, 73.136
Angle α, β, γ (deg.)90.00, 96.94, 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 / Cell (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1A1Q / (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide


Mass: 575.434 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H26Cl2F2N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350, 0.2 M di-Ammonium Citrate

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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: 1.7→50 Å / Num. obs: 67209 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Χ2: 1.001 / Net I/σ(I): 10 / Num. measured all: 433136
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7360.98133570.7160.9130.4241.0711.07999.1
1.73-1.765.90.85433230.7530.9270.3760.9351.09399.7
1.76-1.796.30.70633550.8050.9440.3020.7691.08799.6
1.79-1.836.50.633150.8410.9560.2510.6511.07399.7
1.83-1.876.50.46733560.9050.9750.1970.5081.10699.7
1.87-1.916.20.38533170.9320.9820.1660.421.12499.8
1.91-1.966.20.333520.9590.9890.130.3281.12399.8
1.96-2.026.50.24133730.9720.9930.1010.2611.12799.9
2.02-2.076.30.19433230.980.9950.0830.2121.11899.9
2.07-2.146.30.15533540.9860.9970.0670.1691.11199.9
2.14-2.226.70.12833750.9920.9980.0530.1381.106100
2.22-2.316.70.10333540.9940.9980.0430.1121.078100
2.31-2.416.30.0933450.9950.9990.0390.0981.021100
2.41-2.546.80.07233840.9970.9990.0290.0780.966100
2.54-2.76.50.06133620.9970.9990.0260.0670.941100
2.7-2.916.80.04933520.99810.020.0540.887100
2.91-3.26.70.04134070.99910.0170.0440.805100
3.2-3.666.60.03433650.99910.0140.0370.73499.9
3.66-4.616.60.03133920.99910.0130.0340.68499.8
4.61-506.50.0334480.99810.0130.0320.83899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→48.26 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.012 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20634 3333 5 %RANDOM
Rwork0.17842 ---
obs0.1798 63834 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.504 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-1.17 Å2
2--0.3 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.7→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 0 303 5014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124975
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164425
X-RAY DIFFRACTIONr_angle_refined_deg1.3281.7896793
X-RAY DIFFRACTIONr_angle_other_deg0.481.75710153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5925629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.714525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00310737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021219
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_it1.4772.0432466
X-RAY DIFFRACTIONr_mcbond_other1.4762.0432467
X-RAY DIFFRACTIONr_mcangle_it2.4423.6563102
X-RAY DIFFRACTIONr_mcangle_other2.4413.6563103
X-RAY DIFFRACTIONr_scbond_it1.7322.2412509
X-RAY DIFFRACTIONr_scbond_other1.7322.2412510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7984.0283689
X-RAY DIFFRACTIONr_long_range_B_refined5.1122.555220
X-RAY DIFFRACTIONr_long_range_B_other5.04321.775168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å
RfactorNum. reflection% reflection
Rfree0.302 219 -
Rwork0.294 4524 -
obs--95.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90140.02251.41771.0656-0.13252.26130.165-0.1281-0.01160.0194-0.00030.00130.16610.0082-0.16470.03980.0077-0.00080.0402-0.0050.01943.0518-13.058631.7294
20.7763-0.45360.2982.0947-0.76682.74050.00190.09830.0218-0.23610.020.11870.05810.0446-0.02190.0304-0.0096-0.01820.0193-0.00110.039618.29234.79932.6702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1079 - 1402
2X-RAY DIFFRACTION2B1079 - 1401

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