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

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Basic information

Entry
Database: PDB / ID: 8ogb
TitleCrystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 8
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE / DCAF1 / E3 ligase / compound
Function / homology
Function and homology information


cell competition in a multicellular organism / histone H2AT120 kinase activity / 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 ...cell competition in a multicellular organism / histone H2AT120 kinase activity / 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 / 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
Chem-VN5 / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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)42,4165
Polymers41,7651
Non-polymers6514
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.018, 85.018, 219.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-VN5 / ~{N}'-[2-[1-(4-methoxyphenyl)cyclopropyl]-7-(4-methylpiperazin-1-yl)quinazolin-4-yl]ethane-1,2-diamine


Mass: 432.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H32N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 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 EIGER2 S 16M / Detector: PIXEL / Date: Apr 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→219.36 Å / Num. obs: 22640 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.998 / Net I/σ(I): 14.8
Reflection shellResolution: 2.27→2.34 Å / Num. unique obs: 2016 / CC1/2: 0.784

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→61.206 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.524 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2125 1129 5.007 %
Rwork0.1682 21420 -
all0.17 --
obs-22549 99.951 %
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: 39.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.229 Å2-0.115 Å2-0 Å2
2---0.229 Å20 Å2
3---0.743 Å2
Refinement stepCycle: LAST / Resolution: 2.27→61.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 44 233 2661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0132516
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152275
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.6563417
X-RAY DIFFRACTIONr_angle_other_deg1.461.5795229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3565306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97522.836134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56215407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0911513
X-RAY DIFFRACTIONr_chiral_restr0.0920.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022869
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02602
X-RAY DIFFRACTIONr_nbd_refined0.1930.2417
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.22243
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21173
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2194
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0970.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.29
X-RAY DIFFRACTIONr_nbd_other0.1640.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2280.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0160.21
X-RAY DIFFRACTIONr_mcbond_it2.6172.9471218
X-RAY DIFFRACTIONr_mcbond_other2.62.9461217
X-RAY DIFFRACTIONr_mcangle_it4.1154.4091526
X-RAY DIFFRACTIONr_mcangle_other4.1144.411527
X-RAY DIFFRACTIONr_scbond_it3.223.4461298
X-RAY DIFFRACTIONr_scbond_other3.2193.451299
X-RAY DIFFRACTIONr_scangle_it5.0984.9961888
X-RAY DIFFRACTIONr_scangle_other5.09751889
X-RAY DIFFRACTIONr_lrange_it7.67635.3952759
X-RAY DIFFRACTIONr_lrange_other7.61334.8232705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.3290.302810.2321536X-RAY DIFFRACTION100
2.329-2.3930.288870.2241503X-RAY DIFFRACTION100
2.393-2.4620.276690.2191457X-RAY DIFFRACTION100
2.462-2.5380.308900.2151416X-RAY DIFFRACTION100
2.538-2.6210.248850.1881364X-RAY DIFFRACTION100
2.621-2.7130.288570.1741364X-RAY DIFFRACTION100
2.713-2.8160.225680.1621301X-RAY DIFFRACTION100
2.816-2.930.189560.1631269X-RAY DIFFRACTION100
2.93-3.0610.212670.1441202X-RAY DIFFRACTION100
3.061-3.210.186660.1531138X-RAY DIFFRACTION100
3.21-3.3840.227650.1641104X-RAY DIFFRACTION99.744
3.384-3.5890.206530.1561054X-RAY DIFFRACTION100
3.589-3.8370.199500.15986X-RAY DIFFRACTION99.9036
3.837-4.1440.192400.155945X-RAY DIFFRACTION99.7974
4.144-4.5390.139430.134861X-RAY DIFFRACTION99.8895
4.539-5.0750.172280.141806X-RAY DIFFRACTION99.7608
5.075-5.8590.179290.167710X-RAY DIFFRACTION100
5.859-7.1750.215400.194612X-RAY DIFFRACTION100
7.175-10.1420.176350.169482X-RAY DIFFRACTION100
10.142-61.2060.307200.253310X-RAY DIFFRACTION99.3976
Refinement TLS params.Method: refined / Origin x: -17.2735 Å / Origin y: -35.2045 Å / Origin z: 11.3902 Å
111213212223313233
T0.0062 Å20.0119 Å20.0042 Å2-0.0351 Å20.0087 Å2--0.0173 Å2
L3.3277 °2-0.727 °20.8946 °2-0.5216 °20.0052 °2--0.9761 °2
S-0.0453 Å °-0.0473 Å °0.0697 Å °0.0181 Å °0.0214 Å °0.0545 Å °-0.0574 Å °-0.1525 Å °0.0239 Å °
Refinement TLS groupSelection: ALL

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