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

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Basic information

Entry
Database: PDB / ID: 8ogc
TitleCrystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 11
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE / DCAF1 / E3 ligase / compound
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
ACETATE ION / Chem-VMZ / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSchroeder, M. / Vulpetti, A. / Renatus, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Discovery of New Binders for DCAF1, an Emerging Ligase Target in the Targeted Protein Degradation Field.
Authors: Vulpetti, A. / Holzer, P. / Schmiedeberg, N. / Imbach-Weese, P. / Pissot-Soldermann, C. / Hollingworth, G.J. / Radimerski, T. / Thoma, C.R. / Stachyra, T.M. / Wojtynek, M. / Maschlej, M. / ...Authors: Vulpetti, A. / Holzer, P. / Schmiedeberg, N. / Imbach-Weese, P. / Pissot-Soldermann, C. / Hollingworth, G.J. / Radimerski, T. / Thoma, C.R. / Stachyra, T.M. / Wojtynek, M. / Maschlej, M. / Chau, S. / Schuffenhauer, A. / Fernandez, C. / Schroder, M. / Renatus, M.
History
DepositionMar 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 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)43,0348
Polymers41,7651
Non-polymers1,2697
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-0 kcal/mol
Surface area13450 Å2
Unit cell
Length a, b, c (Å)81.740, 81.740, 234.101
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-1504-

ACT

21A-1504-

ACT

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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 , 6 types, 200 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-VMZ / 1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclopentyl]quinazolin-7-yl]piperazin-1-yl]ethanone


Mass: 493.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33ClN6O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 2.18M Lithium acetate

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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 EIGER2 S 16M / Detector: PIXEL / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→234.1 Å / Num. obs: 28474 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.999 / Net I/σ(I): 14.3
Reflection shellResolution: 2.09→2.15 Å / Num. unique obs: 2159 / CC1/2: 0.746

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→70.889 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.249 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.136
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2015 1412 4.975 %
Rwork0.1713 26969 -
all0.173 --
obs-28381 100 %
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: 34.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.215 Å20.108 Å20 Å2
2--0.215 Å20 Å2
3----0.698 Å2
Refinement stepCycle: LAST / Resolution: 2.09→70.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 87 193 2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0132575
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152291
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.6823498
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5795265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7245307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59822.647136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26515412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0441514
X-RAY DIFFRACTIONr_chiral_restr0.2910.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022922
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02608
X-RAY DIFFRACTIONr_nbd_refined0.1870.2436
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22238
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21217
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2184
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.22
X-RAY DIFFRACTIONr_nbd_other0.1580.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.28
X-RAY DIFFRACTIONr_mcbond_it2.0492.4591224
X-RAY DIFFRACTIONr_mcbond_other2.0392.4561221
X-RAY DIFFRACTIONr_mcangle_it3.2453.6711531
X-RAY DIFFRACTIONr_mcangle_other3.2453.6731532
X-RAY DIFFRACTIONr_scbond_it2.852.9681351
X-RAY DIFFRACTIONr_scbond_other2.6422.8541274
X-RAY DIFFRACTIONr_scangle_it4.3154.3021967
X-RAY DIFFRACTIONr_scangle_other4.0654.1291856
X-RAY DIFFRACTIONr_lrange_it7.32230.7472867
X-RAY DIFFRACTIONr_lrange_other7.10329.5932681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.1440.2521090.2331938X-RAY DIFFRACTION100
2.144-2.2030.262890.2351898X-RAY DIFFRACTION100
2.203-2.2670.2431130.231846X-RAY DIFFRACTION100
2.267-2.3370.2341020.2041774X-RAY DIFFRACTION100
2.337-2.4130.243940.1961740X-RAY DIFFRACTION100
2.413-2.4980.225900.1961683X-RAY DIFFRACTION100
2.498-2.5920.209690.21639X-RAY DIFFRACTION100
2.592-2.6980.24920.1831578X-RAY DIFFRACTION100
2.698-2.8180.188740.1691533X-RAY DIFFRACTION100
2.818-2.9560.183670.161462X-RAY DIFFRACTION100
2.956-3.1160.158690.1511385X-RAY DIFFRACTION100
3.116-3.3050.161680.1481328X-RAY DIFFRACTION100
3.305-3.5330.228510.161264X-RAY DIFFRACTION100
3.533-3.8160.171760.1541153X-RAY DIFFRACTION100
3.816-4.180.163610.1441079X-RAY DIFFRACTION100
4.18-4.6730.157460.129998X-RAY DIFFRACTION100
4.673-5.3950.175460.152900X-RAY DIFFRACTION100
5.395-6.6070.296440.208759X-RAY DIFFRACTION100
6.607-9.340.227310.189622X-RAY DIFFRACTION100
9.34-70.8880.201210.189390X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.9505 Å / Origin y: -31.7845 Å / Origin z: 11.5374 Å
111213212223313233
T0.0497 Å2-0.0089 Å20.0079 Å2-0.0067 Å2-0.0013 Å2--0.0205 Å2
L2.0306 °2-0.5461 °20.1445 °2-1.0897 °20.266 °2--0.8977 °2
S0.0048 Å °0.0583 Å °-0.1497 Å °-0.0448 Å °-0.0043 Å °0.0657 Å °0.0484 Å °-0.0295 Å °-0.0004 Å °
Refinement TLS groupSelection: ALL

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