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- PDB-8r6b: DTX1 WWE domain in complex with ADP bound to WWE2 -

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Basic information

Entry
Database: PDB / ID: 8r6b
TitleDTX1 WWE domain in complex with ADP bound to WWE2
ComponentsE3 ubiquitin-protein ligase DTX1
KeywordsLIGASE / E3 Ligase / Nucleotide / WWE domain / ADP
Function / homology
Function and homology information


negative regulation of T cell differentiation / regulation of Notch signaling pathway / glial cell differentiation / Notch binding / T cell differentiation / negative regulation of neuron differentiation / Notch signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / cellular response to leukemia inhibitory factor / RING-type E3 ubiquitin transferase ...negative regulation of T cell differentiation / regulation of Notch signaling pathway / glial cell differentiation / Notch binding / T cell differentiation / negative regulation of neuron differentiation / Notch signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / cellular response to leukemia inhibitory factor / RING-type E3 ubiquitin transferase / SH3 domain binding / ubiquitin protein ligase activity / transcription by RNA polymerase II / transcription coactivator activity / cell surface receptor signaling pathway / nuclear body / protein ubiquitination / DNA-templated transcription / ubiquitin protein ligase binding / zinc ion binding / nucleoplasm / cytosol / 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'-DIPHOSPHATE / E3 ubiquitin-protein ligase DTX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMuenzker, L. / Zak, K.M. / Boettcher, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)875510European Union
CitationJournal: Commun Biol / Year: 2024
Title: A ligand discovery toolbox for the WWE domain family of human E3 ligases.
Authors: Munzker, L. / Kimani, S.W. / Fowkes, M.M. / Dong, A. / Zheng, H. / Li, Y. / Dasovich, M. / Zak, K.M. / Leung, A.K.L. / Elkins, J.M. / Kessler, D. / Arrowsmith, C.H. / Halabelian, L. / Bottcher, J.
History
DepositionNov 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8272
Polymers19,4001
Non-polymers4271
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.856, 67.372, 70.291
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein E3 ubiquitin-protein ligase DTX1


Mass: 19400.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DTX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86Y01
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.0, 25 % v/v PEG MME 350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999979 Å / Relative weight: 1
ReflectionResolution: 2.5→70.29 Å / Num. obs: 5530 / % possible obs: 92.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 15.83 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.109 / Net I/σ(I): 10.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4 / Num. unique obs: 507 / CC1/2: 0.942 / % possible all: 77.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSFeb 5, 2021data reduction
autoPROC1.1.7data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.15 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 247 4.5 %RANDOM
Rwork0.2208 5236 --
obs0.222 5483 92.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.34 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 27 5 1397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261437
X-RAY DIFFRACTIONf_angle_d0.71461960
X-RAY DIFFRACTIONf_chiral_restr0.0471203
X-RAY DIFFRACTIONf_plane_restr0.0057249
X-RAY DIFFRACTIONf_dihedral_angle_d16.122530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.150.3071180.232362X-RAY DIFFRACTION85.52
3.15-35.150.21741290.21612874X-RAY DIFFRACTION98.65

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