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- PDB-9c1q: Crystal structure of the WDR domain of human DCAF1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9c1q
TitleCrystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / DCAF1 / SGC
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 / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Authorskimani, S. / Dong, A. / Li, Y. / Seitova, A. / Al-awar, R. / Wilson, B. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 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
DepositionMay 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DDB1- and CUL4-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,37912
Polymers35,5931
Non-polymers78611
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.340, 82.340, 233.617
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1651-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.: 1
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

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Non-polymers , 5 types, 211 molecules

#2: Chemical ChemComp-A1ATT / (4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-(3-methoxyprop-1-yn-1-yl)-1H-pyrrole-3-carboxamide


Mass: 506.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19Cl2F2N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M Magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 44430 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Χ2: 0.567 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.8-1.8314.30.9521690.8710.9650.2580.9850.49899.9
1.83-1.8614.20.79521510.9110.9760.2170.8250.51299.9
1.86-1.9140.66521750.9310.9820.1830.690.524100
1.9-1.9413.70.51921560.9570.9890.1440.5390.537100
1.94-1.9812.70.43322010.9620.990.1260.4520.554100
1.98-2.0312.40.35621640.9730.9930.1040.3710.553100
2.03-2.0814.70.3121840.9830.9960.0830.3220.574100
2.08-2.1314.80.25221840.9880.9970.0670.2610.575100
2.13-2.214.80.21321970.9920.9980.0570.2210.572100
2.2-2.2714.60.17822010.9940.9990.0480.1840.592100
2.27-2.3514.50.15121940.9950.9990.0410.1570.59100
2.35-2.4414.30.13621970.9960.9990.0370.1410.591100
2.44-2.55140.11422150.9970.9990.0310.1180.593100
2.55-2.6913.70.08822130.99810.0250.0920.596100
2.69-2.86120.06822400.99910.020.0710.606100
2.86-3.08140.05222280.99910.0140.0540.60299.9
3.08-3.3914.50.0392251110.010.040.59599.8
3.39-3.8813.70.0292263110.0080.030.58499
3.88-4.8812.40.0242317110.0070.0250.53999.3
4.88-50120.0252530110.0070.0260.55699.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.22 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.12 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19136 1377 3.1 %RANDOM
Rwork0.15654 ---
obs0.15759 42962 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: 1 / Resolution: 1.8→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 44 200 2618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122538
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162259
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.7983457
X-RAY DIFFRACTIONr_angle_other_deg0.4521.7615186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.613515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03410388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
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_it6.242.9131242
X-RAY DIFFRACTIONr_mcbond_other6.2032.9131242
X-RAY DIFFRACTIONr_mcangle_it9.5245.2261560
X-RAY DIFFRACTIONr_mcangle_other9.5285.2271561
X-RAY DIFFRACTIONr_scbond_it7.2263.2531296
X-RAY DIFFRACTIONr_scbond_other7.2183.2531295
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.9455.8381897
X-RAY DIFFRACTIONr_long_range_B_refined15.73229.792661
X-RAY DIFFRACTIONr_long_range_B_other15.19929.722626
X-RAY DIFFRACTIONr_rigid_bond_restr2.92734797
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 111 -
Rwork0.194 3077 -
obs--99.84 %

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