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- PDB-8r79: The D2 domain of human DTX3L -

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Basic information

Entry
Database: PDB / ID: 8r79
TitleThe D2 domain of human DTX3L
ComponentsE3 ubiquitin-protein ligase DTX3L
KeywordsLIGASE / Ubiquitin ligase / Homo 4-mer / N-terminal domain
Function / homology
Function and homology information


histone H4K91 ubiquitin ligase activity / protein ADP-ribosyltransferase-substrate adaptor activity / histone ubiquitin ligase activity / positive regulation of protein localization to early endosome / negative regulation of ubiquitin-protein transferase activity / enzyme inhibitor activity / positive regulation of chromatin binding / DNA repair-dependent chromatin remodeling / STAT family protein binding / positive regulation of receptor catabolic process ...histone H4K91 ubiquitin ligase activity / protein ADP-ribosyltransferase-substrate adaptor activity / histone ubiquitin ligase activity / positive regulation of protein localization to early endosome / negative regulation of ubiquitin-protein transferase activity / enzyme inhibitor activity / positive regulation of chromatin binding / DNA repair-dependent chromatin remodeling / STAT family protein binding / positive regulation of receptor catabolic process / endosome to lysosome transport / ubiquitin-like protein ligase binding / protein autoubiquitination / protein K48-linked ubiquitination / Notch signaling pathway / positive regulation of defense response to virus by host / DNA damage checkpoint signaling / RING-type E3 ubiquitin transferase / positive regulation of protein localization to nucleus / ubiquitin-protein transferase activity / double-strand break repair / Antigen processing: Ubiquitination & Proteasome degradation / protein transport / positive regulation of protein binding / early endosome membrane / histone binding / ubiquitin-dependent protein catabolic process / defense response to virus / lysosome / lysosomal membrane / innate immune response / positive regulation of DNA-templated transcription / enzyme binding / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
DTX3L, RING-HC finger / : / : / DTX3L, alpha/beta domain / DTX3L, KH-like domain / Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / Zinc finger, C3HC4 type (RING finger) ...DTX3L, RING-HC finger / : / : / DTX3L, alpha/beta domain / DTX3L, KH-like domain / Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase DTX3L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.18 Å
AuthorsVela-Rodriguez, C. / Lehtio, L. / Maksimainen, M. / Duman, R. / Wagner, A. / Glumoff, T.
Funding support Finland, 1items
OrganizationGrant numberCountry
Other government Finland
CitationJournal: Biorxiv / Year: 2023
Title: Oligomerisation mediated by the D2 domain of DTX3L is critical for DTX3L-PARP9 reading function of mono-ADP-ribosylated androgen receptor.
Authors: Vela-Rodriguez, C. / Yang, C. / Alanen, H.I. / Eki, R. / Abbas, T.A. / Maksimainen, M.M. / Glumoff, T. / Duman, R. / Wagner, A. / Paschal, B.M. / Lehtio, L.
History
DepositionNov 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase DTX3L
B: E3 ubiquitin-protein ligase DTX3L
C: E3 ubiquitin-protein ligase DTX3L
D: E3 ubiquitin-protein ligase DTX3L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0928
Polymers34,7074
Non-polymers3844
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, The molecular weight of a sample subjected to SEC-SAXS corresponded to a tetramer of D2 domains., mass spectrometry, Native mass spectrometry experiments indicated the presence of ...Evidence: SAXS, The molecular weight of a sample subjected to SEC-SAXS corresponded to a tetramer of D2 domains., mass spectrometry, Native mass spectrometry experiments indicated the presence of monomeric, dimeric and tetrameric species.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-120 kcal/mol
Surface area11770 Å2
Unit cell
Length a, b, c (Å)140.893, 140.893, 41.037
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
E3 ubiquitin-protein ligase DTX3L / B-lymphoma- and BAL-associated protein / Protein deltex-3-like / RING-type E3 ubiquitin transferase ...B-lymphoma- and BAL-associated protein / Protein deltex-3-like / RING-type E3 ubiquitin transferase DTX3L / Rhysin-2 / Rhysin2


Mass: 8676.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DTX3L, BBAP / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q8TDB6, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 2.2 M (NH4)2SO4, 100 mM BisTris

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 22, 2021
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 2.18→70.45 Å / Num. obs: 12554 / % possible obs: 91.7 % / Redundancy: 90.6 % / CC1/2: 1 / Rmerge(I) obs: 0.107 / Net I/σ(I): 33.3
Reflection shellResolution: 2.181→2.334 Å / Redundancy: 55.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 628 / CC1/2: 0.842 / % possible all: 67.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
XSCALEdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.18→70.45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.95 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24885 1255 10 %RANDOM
Rwork0.21014 ---
obs0.21428 11299 56.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.896 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-0 Å2
2--0.3 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 2.18→70.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 20 0 1948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131971
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151857
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.6482649
X-RAY DIFFRACTIONr_angle_other_deg1.2391.5894280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58423.243111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8891512
X-RAY DIFFRACTIONr_chiral_restr0.060.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
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_it4.1275.45956
X-RAY DIFFRACTIONr_mcbond_other4.1245.449955
X-RAY DIFFRACTIONr_mcangle_it5.9448.1631188
X-RAY DIFFRACTIONr_mcangle_other5.9418.1641189
X-RAY DIFFRACTIONr_scbond_it5.2046.0571013
X-RAY DIFFRACTIONr_scbond_other5.1786.0561009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7688.8681455
X-RAY DIFFRACTIONr_long_range_B_refined9.44263.282043
X-RAY DIFFRACTIONr_long_range_B_other9.44163.2942044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.181→2.238 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.514 11 -
Rwork0.357 99 -
obs--6.87 %

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