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- PDB-8og9: Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex... -

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Basic information

Entry
Database: PDB / ID: 8og9
TitleCrystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 4
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
Chem-VM3 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.945 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)42,4023
Polymers41,7651
Non-polymers6382
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13600 Å2
Unit cell
Length a, b, c (Å)82.981, 82.981, 237.602
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-1607-

HOH

21A-1611-

HOH

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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: 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
#2: Chemical ChemComp-VM3 / 5-[1-(4-chlorophenyl)cyclopropyl]imidazo[2,1-a]isoquinoline


Mass: 318.800 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H15ClN2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES pH6.5, 2.13M 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 PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→53.277 Å / Num. obs: 11003 / % possible obs: 99.6 % / Redundancy: 18.5 % / CC1/2: 0.994 / Net I/σ(I): 7.2
Reflection shellResolution: 2.94→3.12 Å / Num. unique obs: 1680 / CC1/2: 0.654

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.945→53.277 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 32.72 / SU ML: 0.272 / Cross valid method: FREE R-VALUE / ESU R: 1.126 / ESU R Free: 0.349
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2404 508 4.644 %
Rwork0.1905 10430 -
all0.193 --
obs-10938 99.654 %
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: 57.668 Å2
Baniso -1Baniso -2Baniso -3
1-1.019 Å20.51 Å20 Å2
2--1.019 Å2-0 Å2
3----3.307 Å2
Refinement stepCycle: LAST / Resolution: 2.945→53.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 46 11 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152233
X-RAY DIFFRACTIONr_angle_refined_deg1.481.6693403
X-RAY DIFFRACTIONr_angle_other_deg1.1841.5785135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8685301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31822.782133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.92315403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6031513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
X-RAY DIFFRACTIONr_nbd_refined0.1760.2358
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22030
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21145
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21262
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0510.23
X-RAY DIFFRACTIONr_nbd_other0.1140.217
X-RAY DIFFRACTIONr_mcbond_it1.6944.3391207
X-RAY DIFFRACTIONr_mcbond_other1.6954.3371205
X-RAY DIFFRACTIONr_mcangle_it2.9426.5041507
X-RAY DIFFRACTIONr_mcangle_other2.9416.5041507
X-RAY DIFFRACTIONr_scbond_it1.8634.6921296
X-RAY DIFFRACTIONr_scbond_other1.824.5951243
X-RAY DIFFRACTIONr_scangle_it3.1816.931890
X-RAY DIFFRACTIONr_scangle_other3.1276.7841815
X-RAY DIFFRACTIONr_lrange_it5.09448.662486
X-RAY DIFFRACTIONr_lrange_other5.06148.2142426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.945-3.0210.339430.363707X-RAY DIFFRACTION95.9079
3.021-3.1040.34360.319725X-RAY DIFFRACTION100
3.104-3.1940.264270.27735X-RAY DIFFRACTION100
3.194-3.2920.339290.235677X-RAY DIFFRACTION100
3.292-3.40.281280.223681X-RAY DIFFRACTION100
3.4-3.520.22350.189648X-RAY DIFFRACTION100
3.52-3.6530.285320.175635X-RAY DIFFRACTION100
3.653-3.8020.209280.173616X-RAY DIFFRACTION100
3.802-3.9710.188270.171584X-RAY DIFFRACTION100
3.971-4.1640.188290.149560X-RAY DIFFRACTION100
4.164-4.390.208210.133548X-RAY DIFFRACTION100
4.39-4.6560.171210.121512X-RAY DIFFRACTION100
4.656-4.9770.209270.125482X-RAY DIFFRACTION100
4.977-5.3760.164250.166450X-RAY DIFFRACTION100
5.376-5.8890.247220.189423X-RAY DIFFRACTION100
5.889-6.5830.33250.188385X-RAY DIFFRACTION100
6.583-7.6010.265120.198357X-RAY DIFFRACTION100
7.601-9.3060.206190.19302X-RAY DIFFRACTION100
9.306-13.1510.221160.205243X-RAY DIFFRACTION100
13.151-53.2770.53560.295160X-RAY DIFFRACTION98.2249
Refinement TLS params.Method: refined / Origin x: -15.7246 Å / Origin y: -32.4652 Å / Origin z: 11.4674 Å
111213212223313233
T0.0877 Å20.0036 Å20.0153 Å2-0.0669 Å2-0.0354 Å2--0.0366 Å2
L3.7986 °2-0.8514 °2-0.5067 °2-1.3989 °20.6705 °2--1.6414 °2
S-0.1252 Å °0.0105 Å °-0.2549 Å °0.0469 Å °0.1537 Å °-0.0412 Å °0.1359 Å °0.11 Å °-0.0285 Å °
Refinement TLS groupSelection: ALL

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