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

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Basic information

Entry
Database: PDB / ID: 7sse
TitleCrystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE / WD-repeat / WDR / DCAF1 / SGC / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


histone H2AT120 kinase activity / 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 ...histone H2AT120 kinase activity / 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 / non-specific serine/threonine protein kinase / protein ubiquitination / protein serine kinase activity / 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
Chem-B1I / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKimani, S. / Owen, J. / Li, A. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Shahani, V.M. / Schapira, M. / Arrowsmith, C.H. ...Kimani, S. / Owen, J. / Li, A. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Shahani, V.M. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: 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
DepositionNov 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author / entity_src_gen / Item: _entity_src_gen.gene_src_common_name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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

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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)71,5433
Polymers71,1862
Non-polymers3571
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.956, 87.919, 73.878
Angle α, β, γ (deg.)90.000, 98.720, 90.000
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-B1I / N-[(3R)-1-(3-fluorophenyl)piperidin-3-yl]-6-(morpholin-4-yl)pyrimidin-4-amine


Mass: 357.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24FN5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 44.28 % / Mosaicity: 0.232 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% PEG3350 ,0.1M Ammonium Sulphate, 0.1M Bis-Tris pH5.5

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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: Aug 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 76489 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.024 / Rrim(I) all: 0.048 / Χ2: 1.142 / Net I/σ(I): 13.5 / Num. measured all: 269845
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.652.10.51630680.6660.390.6510.68778.4
1.65-1.682.70.48835790.7440.3340.5950.6691.9
1.68-1.713.40.42438070.8470.2590.4990.68897.4
1.71-1.753.60.35338660.8940.2110.4130.69398.4
1.75-1.783.70.2838120.9320.1650.3260.67799
1.78-1.823.70.22839320.9440.1350.2650.74799.1
1.82-1.873.70.18438710.9670.1090.2140.78499.3
1.87-1.923.60.14338460.9770.0860.1680.82499.1
1.92-1.983.60.11138830.9830.0670.130.87998.8
1.98-2.043.50.09138780.9880.0560.1070.96798.7
2.04-2.113.20.07238540.990.0460.0861.05298
2.11-2.23.80.06538820.9940.0380.0751.02999.5
2.2-2.33.80.05439020.9950.0320.0631.13499.6
2.3-2.423.80.0538920.9960.0290.0581.2299.5
2.42-2.573.80.04839310.9960.0280.0551.39998.8
2.57-2.773.70.04238150.9960.0250.0491.48598.4
2.77-3.053.30.03638860.9970.0220.0421.71197.8
3.05-3.493.90.03538940.9980.020.041.93299
3.49-4.43.90.03339380.9970.0190.0381.9299.4
4.4-503.70.0339530.9970.0180.0351.63798.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PXW

4pxw


Resolution: 1.62→44 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.247 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 3744 4.9 %RANDOM
Rwork0.2056 ---
obs0.2069 72666 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.04 Å2 / Biso mean: 26.441 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å2-0.94 Å2
2---0.24 Å20 Å2
3----0.29 Å2
Refinement stepCycle: final / Resolution: 1.62→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 26 226 4860
Biso mean--35.95 33.14 -
Num. residues----592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134800
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174176
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.6346533
X-RAY DIFFRACTIONr_angle_other_deg1.2831.5789683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9115601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47823.265245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82315739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5211520
X-RAY DIFFRACTIONr_chiral_restr0.0560.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021045
LS refinement shellResolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 203 -
Rwork0.332 4431 -
all-4634 -
obs--80.4 %

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