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- PDB-8ood: Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex... -

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Basic information

Entry
Database: PDB / ID: 8ood
TitleCrystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE / DCAF1 / Ligase / compound
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 / Armadillo-like helical / Armadillo-type fold / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-VY3 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.497 Å
AuthorsSchroeder, M. / Renatus, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biorxiv / Year: 2023
Title: Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings
Authors: Schroder, M. / Renatus, M. / Thoma, C.R.
History
DepositionApr 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)43,87411
Polymers41,7651
Non-polymers2,11010
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint5 kcal/mol
Surface area13320 Å2
Unit cell
Length a, b, c (Å)81.496, 81.496, 232.723
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1502-

ACT

21A-1502-

ACT

31A-1609-

HOH

41A-1902-

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: 41764.824 Da / Num. of mol.: 1 / Mutation: Q1250L
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, 326 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-VY3 / ~{N}-[2-[2-[2-[2-[2-[2-[3-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethyl]ethanamide


Mass: 828.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H62ClN7O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.13M LiSO4, 0.1M Tris pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.497→52.259 Å / Num. obs: 74179 / % possible obs: 99.6 % / Redundancy: 8.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.033 / Rrim(I) all: 0.097 / Χ2: 0.86 / Net I/σ(I): 11.1
Reflection shellResolution: 1.5→1.52 Å / % possible obs: 94 % / Redundancy: 7.9 % / Rmerge(I) obs: 1.726 / Num. measured all: 26759 / Num. unique obs: 3405 / CC1/2: 0.452 / Rpim(I) all: 0.652 / Rrim(I) all: 1.852 / Χ2: 0.79 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.497→52.259 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.23 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.186 3672 4.955 %
Rwork0.17 70438 -
all0.171 --
obs-74110 99.557 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.224 Å20.112 Å20 Å2
2--0.224 Å2-0 Å2
3----0.728 Å2
Refinement stepCycle: LAST / Resolution: 1.497→52.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 104 316 2804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0132788
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152468
X-RAY DIFFRACTIONr_angle_refined_deg2.51.73804
X-RAY DIFFRACTIONr_angle_other_deg1.6151.5785685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9825342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76522.042142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46515445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3771517
X-RAY DIFFRACTIONr_chiral_restr0.3650.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023200
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02659
X-RAY DIFFRACTIONr_nbd_refined0.2030.2509
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.22427
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21242
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.150.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0680.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.29
X-RAY DIFFRACTIONr_nbd_other0.1720.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2070.227
X-RAY DIFFRACTIONr_mcbond_it1.4871.2981313
X-RAY DIFFRACTIONr_mcbond_other1.4641.2961310
X-RAY DIFFRACTIONr_mcangle_it2.4071.9361672
X-RAY DIFFRACTIONr_mcangle_other2.4091.9371673
X-RAY DIFFRACTIONr_scbond_it2.5631.7441475
X-RAY DIFFRACTIONr_scbond_other2.441.6271357
X-RAY DIFFRACTIONr_scangle_it3.7872.4762132
X-RAY DIFFRACTIONr_scangle_other3.6052.3071967
X-RAY DIFFRACTIONr_lrange_it6.88418.1783227
X-RAY DIFFRACTIONr_lrange_other6.71216.7462928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.497-1.5360.3812670.3684964X-RAY DIFFRACTION96.6556
1.536-1.5780.3292530.3255001X-RAY DIFFRACTION99.9619
1.578-1.6240.282400.2834892X-RAY DIFFRACTION99.9221
1.624-1.6740.2362310.2384721X-RAY DIFFRACTION99.8387
1.674-1.7290.2392440.24589X-RAY DIFFRACTION99.8967
1.729-1.790.1972380.1674448X-RAY DIFFRACTION99.8934
1.79-1.8570.1842310.1594323X-RAY DIFFRACTION99.9342
1.857-1.9330.1722150.1564135X-RAY DIFFRACTION99.9081
1.933-2.0190.1852300.163950X-RAY DIFFRACTION99.8328
2.019-2.1180.1761970.1583792X-RAY DIFFRACTION99.4019
2.118-2.2320.2011940.1593641X-RAY DIFFRACTION99.8698
2.232-2.3680.1581730.153484X-RAY DIFFRACTION99.918
2.368-2.5310.1671880.1433233X-RAY DIFFRACTION99.8832
2.531-2.7340.1711630.153057X-RAY DIFFRACTION99.845
2.734-2.9950.1651300.1472844X-RAY DIFFRACTION99.6649
2.995-3.3480.1461200.152568X-RAY DIFFRACTION99.5924
3.348-3.8660.1331260.1432301X-RAY DIFFRACTION99.9177
3.866-4.7340.1571030.1381973X-RAY DIFFRACTION99.6639
4.734-6.6940.22840.1971566X-RAY DIFFRACTION99.2183
6.694-52.2590.278450.245954X-RAY DIFFRACTION98.8131
Refinement TLS params.Method: refined / Origin x: -14.9699 Å / Origin y: -31.6907 Å / Origin z: 11.4333 Å
111213212223313233
T0.0342 Å2-0.0087 Å20.0024 Å2-0.0035 Å2-0.0033 Å2--0.0105 Å2
L1.4341 °2-0.5092 °20.1194 °2-0.8527 °20.153 °2--0.645 °2
S0.0064 Å °0.0382 Å °-0.112 Å °-0.0287 Å °-0.0013 Å °0.0666 Å °0.0484 Å °-0.0152 Å °-0.0051 Å °
Refinement TLS groupSelection: ALL

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