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- PDB-8og7: Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex... -

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Basic information

Entry
Database: PDB / ID: 8og7
TitleCrystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 2
ComponentsDDB1- and CUL4-associated factor 1
KeywordsTRANSFERASE / DCAF1 / E3 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-VMR / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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)42,1734
Polymers41,7651
Non-polymers4083
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint2 kcal/mol
Surface area13690 Å2
Unit cell
Length a, b, c (Å)81.750, 81.750, 235.633
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-1501-

ACT

21A-1501-

ACT

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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-ACT / ACETATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-VMR / (4~{R})-4-[3-(4-chloranylphenoxy)phenyl]pyrrolidin-2-imine


Mass: 286.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15ClN2O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
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: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→52.64 Å / Num. obs: 13467 / % possible obs: 94.4 % / Redundancy: 13.3 % / CC1/2: 0.994 / Net I/σ(I): 11.1
Reflection shellResolution: 2.64→2.77 Å / Num. unique obs: 1764 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→52.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 15.88 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.454 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20598 682 5.1 %RANDOM
Rwork0.15759 ---
obs0.16006 12784 92.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.697 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å2-0 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 2.64→52.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 28 162 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152264
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.6493391
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5785200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7355306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27522.353136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77415406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3681515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022873
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
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_it2.293.0741219
X-RAY DIFFRACTIONr_mcbond_other2.2893.0731217
X-RAY DIFFRACTIONr_mcangle_it3.8054.5921526
X-RAY DIFFRACTIONr_mcangle_other3.8044.5941527
X-RAY DIFFRACTIONr_scbond_it2.8733.5591280
X-RAY DIFFRACTIONr_scbond_other2.63.4371259
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.265.011836
X-RAY DIFFRACTIONr_long_range_B_refined7.56535.4852549
X-RAY DIFFRACTIONr_long_range_B_other6.83934.72505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.64→2.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 49 -
Rwork0.252 932 -
obs--94.87 %
Refinement TLS params.Method: refined / Origin x: -14.6828 Å / Origin y: -31.8272 Å / Origin z: 11.6283 Å
111213212223313233
T0.1359 Å20.0258 Å20.0388 Å2-0.0172 Å20.0032 Å2--0.0336 Å2
L3.9449 °2-0.4725 °2-0.0005 °2-1.8974 °20.5135 °2--1.033 °2
S-0.055 Å °0.0665 Å °-0.3118 Å °-0.1907 Å °0.0395 Å °0.0012 Å °0.0728 Å °-0.0186 Å °0.0155 Å °

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