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- PDB-6y22: RING-DTC domains of Deltex 2, Form 1 -

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Basic information

Entry
Database: PDB / ID: 6y22
TitleRING-DTC domains of Deltex 2, Form 1
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. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Probable E3 ubiquitin-protein ligase DTX2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.069 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 14, 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)26,0653
Polymers25,9341
Non-polymers1312
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.418, 106.418, 74.669
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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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: 4.87 Å3/Da / Density % sol: 74.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Morpheus condition 60: 0.12 M ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1 M Buffer system 3 (1 M Tris-Bicine ...Details: Morpheus condition 60: 0.12 M ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol), 0.1 M Buffer system 3 (1 M Tris-Bicine pH 8.5), 37.5% Precipitation mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97997 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97997 Å / Relative weight: 1
ReflectionResolution: 2.069→92.16 Å / Num. obs: 29929 / % possible obs: 99.7 % / Observed criterion σ(F): 1.36 / Redundancy: 10 % / Biso Wilson estimate: 38.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.037 / Net I/σ(I): 16.5
Reflection shellResolution: 2.069→2.12 Å / Redundancy: 10 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2130 / CC1/2: 0.973 / Rpim(I) all: 0.36 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2142refinement
DIALSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.069→29.008 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.06
RfactorNum. reflection% reflection
Rfree0.2083 1434 4.79 %
Rwork0.1793 --
obs0.1807 29926 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.23 Å2 / Biso mean: 55.9843 Å2 / Biso min: 28.87 Å2
Refinement stepCycle: final / Resolution: 2.069→29.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 2 92 1816
Biso mean--48.58 55.29 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061785
X-RAY DIFFRACTIONf_angle_d0.8362430
X-RAY DIFFRACTIONf_chiral_restr0.053272
X-RAY DIFFRACTIONf_plane_restr0.005318
X-RAY DIFFRACTIONf_dihedral_angle_d14.1581076
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.069-2.1430.3218970.2863277597
2.143-2.22870.29971460.2384279099
2.2287-2.33010.28911640.2305280999
2.3301-2.45290.261810.21212791100
2.4529-2.60650.26261580.20542819100
2.6065-2.80760.22921340.19622841100
2.8076-3.08990.22981180.21112897100
3.0899-3.53630.20921240.18612887100
3.5363-4.45280.18071540.14682887100
4.4528-29.0080.17161580.15252996100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.19410.1090.47472.6328-1.16583.04590.22040.14710.0594-0.2275-0.05550.1292-0.03750.0839-0.13660.48420.21770.00960.74680.01340.412525.450544.386812.9384
21.9215-0.1724-0.59681.34380.55144.69130.1231-0.1090.17620.01520.02380.0209-0.5396-0.4802-0.13180.31470.0748-0.01190.30880.01880.318444.406934.953436.1854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 391 through 480 )A391 - 480
2X-RAY DIFFRACTION2chain 'A' and (resid 481 through 616 )A481 - 616

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