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- PDB-8f8e: Crystal structure of the WDR domain of human DCAF1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8f8e
TitleCrystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE/INHIBITOR / WD-repeat / WDR / DCAF1 / SGC / TRANSFERASE / Structural Genomics / Structural Genomics Consortium / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


cell competition in a multicellular organism / 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 ...cell competition in a multicellular organism / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily ...VPRBP/DCAF1 family / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-XJI / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKimani, S. / Li, A. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Wilson, B. / Al-Awar, R. / Vedadi, M. / Brown, P. ...Kimani, S. / Li, A. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Wilson, B. / Al-Awar, R. / Vedadi, M. / Brown, P. / 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 WDR domain of human DCAF1 in complex with OICR-8268 compound
Authors: Kimani, S. / Li, A. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Wilson, B. / Al-Awar, R. / Vedadi, M. / Brown, P. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionNov 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)72,2575
Polymers71,1862
Non-polymers1,0713
Water5,891327
1
A: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0322
Polymers35,5931
Non-polymers4391
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)36,2243
Polymers35,5931
Non-polymers6312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.865, 88.084, 73.562
Angle α, β, γ (deg.)90.00, 97.56, 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 / Mutation: F1077A, R1079A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCAF1, KIAA0800, RIP, VPRBP / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-XJI / (3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide


Mass: 439.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14Cl2F2N4O2 / 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.: 327 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.2M di-Ammonium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 88118 / % possible obs: 98.4 % / Redundancy: 5.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.031 / Rrim(I) all: 0.072 / Net I/σ(I): 27.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starΧ2% possible all
1.55-1.585.10.7481.8844070.7950.9410.68198.7
1.58-1.615.50.67743900.70199
1.61-1.645.60.60287410.71498.8
1.64-1.675.60.51643860.73298.9
1.67-1.715.50.42344020.77398.5
1.71-1.755.40.31143910.81398.2
1.75-1.794.90.28343280.88797.3
1.79-1.845.40.24744650.97499.1
1.84-1.895.60.20444651.05199.1
1.89-1.955.60.17144331.14299.3
1.95-2.025.40.13944281.24798.9
2.02-2.15.30.11844171.40299
2.1-2.25.30.09644251.51498.8
2.2-2.325.10.08343931.54997.6
2.32-2.464.90.07243691.59197.6
2.46-2.654.90.06643631.69897.6
2.65-2.925.50.05944001.83697.9
2.92-3.345.40.05343602.97197
3.34-4.215.40.04743942.09497.4
4.21-50.015.50.04433961.81698

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PXW

4pxw


Resolution: 1.55→44.08 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.702 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20898 1744 2 %RANDOM
Rwork0.18123 ---
obs0.1818 86348 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å2-1.5 Å2
2--0.12 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.55→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 71 327 5018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134938
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174299
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.636745
X-RAY DIFFRACTIONr_angle_other_deg1.3681.5769977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8225625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76123.24250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09615763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6981521
X-RAY DIFFRACTIONr_chiral_restr0.0680.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021081
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_it1.7662.3612426
X-RAY DIFFRACTIONr_mcbond_other1.7652.362423
X-RAY DIFFRACTIONr_mcangle_it2.7893.5343039
X-RAY DIFFRACTIONr_mcangle_other2.793.5343039
X-RAY DIFFRACTIONr_scbond_it2.2492.5882512
X-RAY DIFFRACTIONr_scbond_other2.2482.5862509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4923.793695
X-RAY DIFFRACTIONr_long_range_B_refined4.95628.0195136
X-RAY DIFFRACTIONr_long_range_B_other4.91727.8445086
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: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
14loose positional0.015
18tight thermal3.160.5
14loose thermal2.4110
LS refinement shellResolution: 1.55→1.589 Å
RfactorNum. reflection% reflection
Rfree0.293 118 -
Rwork0.273 6249 -
obs--96.27 %

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