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- PDB-7ufv: Crystal structure of the WDR domain of human DCAF1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7ufv
TitleCrystal structure of the WDR domain of human DCAF1 in complex with OICR-6766
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE / WD-repeat / WDR / DCAF1 / SGC / Structural Genomics / Structural Genomics Consortium
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 / B cell differentiation / post-translational protein modification / 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 / B cell differentiation / post-translational protein modification / 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
Chem-N6O / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsKimani, S. / Li, A. / Li, Y. / Dong, A. / Hutchinson, A. / Seitova, A. / Wilson, B. / Al-Awar, R. / Vedadi, M. / Brown, P. ...Kimani, S. / Li, A. / Li, Y. / Dong, A. / 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 support1items
OrganizationGrant numberCountry
Other private
Citation
Journal: J.Med.Chem. / Year: 2023
Title: Discovery of Nanomolar DCAF1 Small Molecule Ligands.
Authors: Li, A.S.M. / Kimani, S. / Wilson, B. / Noureldin, M. / Gonzalez-Alvarez, H. / Mamai, A. / Hoffer, L. / Guilinger, J.P. / Zhang, Y. / von Rechenberg, M. / Disch, J.S. / Mulhern, C.J. / ...Authors: Li, A.S.M. / Kimani, S. / Wilson, B. / Noureldin, M. / Gonzalez-Alvarez, H. / Mamai, A. / Hoffer, L. / Guilinger, J.P. / Zhang, Y. / von Rechenberg, M. / Disch, J.S. / Mulhern, C.J. / Slakman, B.L. / Cuozzo, J.W. / Dong, A. / Poda, G. / Mohammed, M. / Saraon, P. / Mittal, M. / Modh, P. / Rathod, V. / Patel, B. / Ackloo, S. / Santhakumar, V. / Szewczyk, M.M. / Barsyte-Lovejoy, D. / Arrowsmith, C.H. / Marcellus, R. / Guie, M.A. / Keefe, A.D. / Brown, P.J. / Halabelian, L. / Al-Awar, R. / Vedadi, M.
#1: Journal: J.Chem.Inf.Model. / Year: 2023
Title: Discovery of a Novel DCAF1 Ligand Using a Drug-Target Interaction Prediction Model: Generalizing Machine Learning to New Drug Targets.
Authors: Kimani, S.W. / Owen, J. / Green, S.R. / Li, F. / Li, Y. / Dong, A. / Brown, P.J. / Ackloo, S. / Kuter, D. / Yang, C. / MacAskill, M. / MacKinnon, S.S. / Arrowsmith, C.H. / Schapira, M. / ...Authors: Kimani, S.W. / Owen, J. / Green, S.R. / Li, F. / Li, Y. / Dong, A. / Brown, P.J. / Ackloo, S. / Kuter, D. / Yang, C. / MacAskill, M. / MacKinnon, S.S. / Arrowsmith, C.H. / Schapira, M. / Shahani, V. / Halabelian, L.
History
DepositionMar 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 3, 2024Group: Database references / Category: citation / citation_author

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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)72,3465
Polymers71,1862
Non-polymers1,1603
Water1,58588
1
A: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9802
Polymers35,5931
Non-polymers3871
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)36,3673
Polymers35,5931
Non-polymers7742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.140, 87.875, 73.807
Angle α, β, γ (deg.)90.00, 98.54, 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-N6O / (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide


Mass: 386.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16ClFN4O2
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 386.807 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.21 Å3/Da / Density % sol: 44.44 % / Mosaicity: 0.18 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 20% PEG3350, 0.2M Potassium Fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→43.98 Å / Num. obs: 48379 / % possible obs: 99 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.036 / Rrim(I) all: 0.072 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.943.80.9231189731070.7260.5341.071.599.5
9.11-43.943.70.04617224600.9970.0260.05325.197.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7SSE

7sse


Resolution: 1.9→43.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.386 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2355 4.9 %RANDOM
Rwork0.204 ---
obs0.207 46002 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å2-4.11 Å2
2---0.44 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4553 0 55 88 4696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134717
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174077
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.636414
X-RAY DIFFRACTIONr_angle_other_deg1.2061.5799425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5055582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18523.234235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81715708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5671520
X-RAY DIFFRACTIONr_chiral_restr0.050.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021037
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 145 -
Rwork0.365 3420 -
obs--99.44 %

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