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- PDB-8r6a: DTX1 WWE domain in complex with ADP bound to WWE1 -

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Basic information

Entry
Database: PDB / ID: 8r6a
TitleDTX1 WWE domain in complex with ADP bound to WWE1
ComponentsE3 ubiquitin-protein ligase DTX1
KeywordsLIGASE / WWE domain
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 / cellular response to leukemia inhibitory factor / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / cellular response to leukemia inhibitory factor / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / protein ubiquitination / nuclear body / 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: 2.4 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
B: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6544
Polymers38,8002
Non-polymers8542
Water2,000111
1
A: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8272
Polymers19,4001
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8272
Polymers19,4001
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.080, 34.059, 84.578
Angle α, β, γ (deg.)90.000, 89.982, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 20 through 47 or (resid 48...
d_2ens_1(chain "B" and (resid 20 through 164 or (resid 165...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYSERSERAA20 - 1831 - 164
d_12ADPADPADPADPAC201
d_21GLYGLYSERSERBB20 - 1831 - 164
d_22ADPADPADPADPBD201

NCS oper: (Code: givenMatrix: (-0.999996780043, 0.00233841971642, 0.000985746729775), (-0.00233750537461, -0.999996837719, 0.000927696442905), (0.00098791295622, 0.000925389267484, 0.999999083841) ...NCS oper: (Code: given
Matrix: (-0.999996780043, 0.00233841971642, 0.000985746729775), (-0.00233750537461, -0.999996837719, 0.000927696442905), (0.00098791295622, 0.000925389267484, 0.999999083841)
Vector: 34.0653229432, 3.53002720198, 42.3018506268)

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Components

#1: Protein E3 ubiquitin-protein ligase DTX1


Mass: 19400.014 Da / Num. of mol.: 2
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.: 2 / 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.: 111 / 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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 278 K / Method: vapor diffusion / 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: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→68.68 Å / Num. obs: 15556 / % possible obs: 95.3 % / Redundancy: 2.25 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.25
Reflection shellResolution: 2.4→2.45 Å / Num. unique obs: 892 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→53.03 Å / SU ML: 0.4693 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.3459
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.309 735 4.89 %RANDOM
Rwork0.2712 14298 --
obs0.2732 15033 96.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→53.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 54 111 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282839
X-RAY DIFFRACTIONf_angle_d0.73443870
X-RAY DIFFRACTIONf_chiral_restr0.0475400
X-RAY DIFFRACTIONf_plane_restr0.0046491
X-RAY DIFFRACTIONf_dihedral_angle_d17.26461040
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.627279058513 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.580.37531450.3532570X-RAY DIFFRACTION88.21
2.59-2.850.37031390.32572844X-RAY DIFFRACTION95.49
2.85-3.260.38041330.29632914X-RAY DIFFRACTION98.96
3.26-4.10.37361440.25772928X-RAY DIFFRACTION98.94
4.1-53.030.22971740.23743042X-RAY DIFFRACTION98.68

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