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- PDB-6y3j: RING-DTC domains of Deltex 2, bound to ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 6y3j
TitleRING-DTC domains of Deltex 2, bound to ADP-ribose
ComponentsProbable E3 ubiquitin-protein ligase DTX2
KeywordsLIGASE / Ubiquitination / E3 RING ligase / Ubiquitin / PAR-binding
Function / homology
Function and homology information


Notch signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / nuclear membrane / protein ubiquitination / zinc ion binding / nucleoplasm / cytoplasm
Similarity search - Function
Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. ...Deltex, C-terminal / Deltex family / Deltex, C-terminal domain superfamily / Deltex C-terminal domain / WWE domain, subgroup / Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. / WWE domain / WWE domain superfamily / WWE domain / WWE domain profile. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Probable E3 ubiquitin-protein ligase DTX2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGabrielssen, M. / Buetow, L. / Huang, D.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKA23278 United Kingdom
European Research Council (ERC)647849 United Kingdom
CitationJournal: Sci Adv / Year: 2020
Title: DELTEX2 C-terminal domain recognizes and recruits ADP-ribosylated proteins for ubiquitination.
Authors: Ahmed, S.F. / Buetow, L. / Gabrielsen, M. / Lilla, S. / Chatrin, C. / Sibbet, G.J. / Zanivan, S. / Huang, D.T.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable E3 ubiquitin-protein ligase DTX2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6254
Polymers25,9341
Non-polymers6903
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area11870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.933, 104.933, 74.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Probable E3 ubiquitin-protein ligase DTX2 / Protein deltex-2 / hDTX2 / RING finger protein 58 / RING-type E3 ubiquitin transferase DTX2


Mass: 25934.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DTX2, KIAA1528, RNF58 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86UW9, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.32 Å3/Da / Density % sol: 73.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: Morpheus condition 39 (Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.6→90.87 Å / Num. obs: 27953 / % possible obs: 100 % / Observed criterion σ(F): 1.33 / Redundancy: 9.3 % / Biso Wilson estimate: 43.61 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.137 / Net I/σ(I): 5.3
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 1.618 / Mean I/σ(I) obs: 1 / Num. unique obs: 1792 / CC1/2: 0.822 / Rpim(I) all: 1.791 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALS1.15.2_3472data collection
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y22

6y22


Resolution: 2.6→45.44 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 1303 4.66 %
Rwork0.2376 26650 -
obs0.2398 27953 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.05 Å2 / Biso mean: 58.0141 Å2 / Biso min: 22.26 Å2
Refinement stepCycle: final / Resolution: 2.6→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 38 15 1790
Biso mean--56.94 49.41 -
Num. residues----227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70.45061720.41722903307599
2.7-2.830.41041060.39582997310399
2.83-2.980.41210.35423011313298
2.98-3.160.35271090.2942966307599
3.16-3.410.31181640.26422939310399
3.41-3.750.2981840.22592938312299
3.75-4.290.25421310.1912962309399
4.29-5.40.22241710.17822940311199
5.41-45.440.20011450.171729943139100
Refinement TLS params.Method: refined / Origin x: 36.2615 Å / Origin y: 37.5413 Å / Origin z: 27.1934 Å
111213212223313233
T0.4806 Å20.2311 Å2-0.0061 Å2-0.766 Å20.0624 Å2--0.2504 Å2
L0.9238 °2-0.3855 °20.3842 °2-0.7814 °2-0.0714 °2--0.2505 °2
S0.0894 Å °0.1362 Å °-0.004 Å °0.0696 Å °0.0185 Å °0.0542 Å °-0.6381 Å °-0.8197 Å °-0.0197 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA390 - 616
2X-RAY DIFFRACTION1allA701
3X-RAY DIFFRACTION1allB1 - 2
4X-RAY DIFFRACTION1allS1 - 22

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