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- PDB-6y5n: RING-DTC domain of Deltex1 -

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Basic information

Entry
Database: PDB / ID: 6y5n
TitleRING-DTC domain of Deltex1
ComponentsE3 ubiquitin-protein ligase DTX1
KeywordsLIGASE / Ubiquitination / E3 RING ligase / NAD binding
Function / homology
Function and homology information


regulation of Notch signaling pathway / Notch binding / negative regulation of neuron differentiation / Notch signaling pathway / 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 ...regulation of Notch signaling pathway / Notch binding / negative regulation of neuron differentiation / Notch signaling pathway / 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 / 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. / 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
E3 ubiquitin-protein ligase DTX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsGabrielsen, 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: Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases.
Authors: Chatrin, C. / Gabrielsen, M. / Buetow, L. / Nakasone, M.A. / Ahmed, S.F. / Sumpton, D. / Sibbet, G.J. / Smith, B.O. / Huang, D.T.
History
DepositionFeb 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)52,59610
Polymers52,1392
Non-polymers4578
Water9,368520
1
A: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3606
Polymers26,0701
Non-polymers2905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2364
Polymers26,0701
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.490, 86.550, 129.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 388 through 429 or resid 431...
21(chain B and (resid 388 through 439 or resid 441 through 598 or resid 600 through 615))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSARGARG(chain A and (resid 388 through 429 or resid 431...AA388 - 4293 - 44
12LYSLYSGLYGLY(chain A and (resid 388 through 429 or resid 431...AA431 - 43946 - 54
13LEULEUALAALA(chain A and (resid 388 through 429 or resid 431...AA441 - 59856 - 213
14TYRTYRGLUGLU(chain A and (resid 388 through 429 or resid 431...AA600 - 615215 - 230
21LYSLYSGLYGLY(chain B and (resid 388 through 439 or resid 441 through 598 or resid 600 through 615))BB388 - 4393 - 54
22LEULEUALAALA(chain B and (resid 388 through 439 or resid 441 through 598 or resid 600 through 615))BB441 - 59856 - 213
23TYRTYRGLUGLU(chain B and (resid 388 through 439 or resid 441 through 598 or resid 600 through 615))BB600 - 615215 - 230

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Components

#1: Protein E3 ubiquitin-protein ligase DTX1 / Protein deltex-1 / hDTX1 / RING-type E3 ubiquitin transferase DTX1


Mass: 26069.744 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, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: BCS condition 44 (Molecular dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.88→36.01 Å / Num. obs: 62617 / % possible obs: 100 % / Observed criterion σ(F): 1.92 / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.048 / Net I/σ(I): 14.7
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4576 / CC1/2: 0.629 / Rpim(I) all: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
autoPROCdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→36.007 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 5833 4.9 %
Rwork0.1871 113236 -
obs0.1882 62539 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.46 Å2 / Biso mean: 44.1315 Å2 / Biso min: 19.36 Å2
Refinement stepCycle: final / Resolution: 1.88→36.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3566 0 26 526 4118
Biso mean--60.01 48.67 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113685
X-RAY DIFFRACTIONf_angle_d1.0794989
X-RAY DIFFRACTIONf_chiral_restr0.07536
X-RAY DIFFRACTIONf_plane_restr0.008654
X-RAY DIFFRACTIONf_dihedral_angle_d11.8722222
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2667X-RAY DIFFRACTION14.069TORSIONAL
12B2667X-RAY DIFFRACTION14.069TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.90140.38572000.34643729100
1.9014-1.92370.34811960.33033831100
1.9237-1.94720.34641870.31763764100
1.9472-1.97180.32792230.307374999
1.9718-1.99780.32612120.2893794100
1.9978-2.02510.31461880.29163756100
2.0251-2.05410.31951710.2622372899
2.0541-2.08470.27182000.25133783100
2.0847-2.11730.27281750.24583797100
2.1173-2.1520.2792000.24133801100
2.152-2.18910.25762260.23573700100
2.1891-2.22890.24911640.2097382799
2.2289-2.27180.22281710.20323780100
2.2718-2.31810.25322000.19843811100
2.3181-2.36850.19931960.19493762100
2.3685-2.42360.24351890.1993777100
2.4236-2.48420.25381960.19843801100
2.4842-2.55140.25181680.1983816100
2.5514-2.62640.20711900.18863752100
2.6264-2.71120.21992130.17483787100
2.7112-2.8080.21571870.18093788100
2.808-2.92040.22091800.17363748100
2.9204-3.05330.18721960.18543792100
3.0533-3.21420.20872180.17343773100
3.2142-3.41540.19652020.1675372899
3.4154-3.67890.18291900.16143787100
3.6789-4.04860.14921880.15133806100
4.0486-4.63340.18451960.13643740100
4.6334-5.83360.1652150.15023760100
5.8336-36.0070.1791960.2039376999
Refinement TLS params.Method: refined / Origin x: 72.7526 Å / Origin y: 48.5111 Å / Origin z: 11.1807 Å
111213212223313233
T0.2662 Å20.0053 Å20.0151 Å2-0.2453 Å20.0078 Å2--0.261 Å2
L0.8488 °20.2707 °2-0.2916 °2-0.1611 °2-0.265 °2--0.8583 °2
S-0.0832 Å °-0.0221 Å °-0.1773 Å °-0.1065 Å °0.027 Å °-0.0501 Å °0.2127 Å °-0.0163 Å °0.0442 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA388 - 615
2X-RAY DIFFRACTION1allB388 - 615
3X-RAY DIFFRACTION1allC1 - 4
4X-RAY DIFFRACTION1allD1 - 2
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allS1 - 526

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