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- PDB-6y5p: RING-DTC domain of Deltex1 bound to NAD -

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Basic information

Entry
Database: PDB / ID: 6y5p
TitleRING-DTC domain of Deltex1 bound to NAD
ComponentsE3 ubiquitin-protein ligase DTX1
KeywordsLIGASE / Ubiquitination / E3 RING ligase / NAD binding
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
Enolase-like; domain 1 - #130 / 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 ...Enolase-like; domain 1 - #130 / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Enolase-like; domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / E3 ubiquitin-protein ligase DTX1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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 1.1Jan 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 / 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)54,22516
Polymers52,1392
Non-polymers2,08514
Water7,566420
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A: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,23610
Polymers26,0701
Non-polymers1,1679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase DTX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9886
Polymers26,0701
Non-polymers9185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.850, 85.254, 130.949
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 535 or resid 537 through 598 or resid 600 through 615))
21(chain B and (resid 388 through 535 or resid 537 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
11LYSLYSHISHIS(chain A and (resid 388 through 535 or resid 537 through 598 or resid 600 through 615))AA388 - 5353 - 150
12TYRTYRALAALA(chain A and (resid 388 through 535 or resid 537 through 598 or resid 600 through 615))AA537 - 598152 - 213
13TYRTYRGLUGLU(chain A and (resid 388 through 535 or resid 537 through 598 or resid 600 through 615))AA600 - 615215 - 230
21LYSLYSHISHIS(chain B and (resid 388 through 535 or resid 537 through 598 or resid 600 through 615))BB388 - 5353 - 150
22TYRTYRALAALA(chain B and (resid 388 through 535 or resid 537 through 598 or resid 600 through 615))BB537 - 598152 - 213
23TYRTYRGLUGLU(chain B and (resid 388 through 535 or resid 537 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 420 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.16M Calcium acetate hydrate, 0.08MSodium cacodylate pH 6.5, 14.4% w/v PEG 8000, 20% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.74→66.85 Å / Num. obs: 148052 / % possible obs: 100 % / Observed criterion σ(F): 1.33 / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Net I/σ(I): 16
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.334 / Mean I/σ(I) obs: 1 / Num. unique obs: 5662 / CC1/2: 0.521 / Rpim(I) all: 0.898 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y5N

6y5n


Resolution: 1.74→65.475 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 7180 4.85 %
Rwork0.1853 140872 -
obs0.1867 148052 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.3 Å2 / Biso mean: 44.4615 Å2 / Biso min: 18.51 Å2
Refinement stepCycle: final / Resolution: 1.74→65.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 224 420 4225
Biso mean--63.59 46.86 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013812
X-RAY DIFFRACTIONf_angle_d1.1035170
X-RAY DIFFRACTIONf_chiral_restr0.059554
X-RAY DIFFRACTIONf_plane_restr0.008665
X-RAY DIFFRACTIONf_dihedral_angle_d12.6132244
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2675X-RAY DIFFRACTION13.616TORSIONAL
12B2675X-RAY DIFFRACTION13.616TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.74-1.75970.3272700.3412465198
1.7597-1.78040.33682390.3248461399
1.7804-1.80210.35332520.31334712100
1.8021-1.82490.34912340.30734622100
1.8249-1.84890.29782570.30084732100
1.8489-1.87420.31882080.29144705100
1.8742-1.9010.30022710.27654722100
1.901-1.92940.25732020.26054729100
1.9294-1.95950.25732300.24334707100
1.9595-1.99170.21392100.23794658100
1.9917-2.0260.24612580.22054742100
2.026-2.06290.22522310.21244677100
2.0629-2.10250.24132550.21094685100
2.1025-2.14540.23062080.20114749100
2.1454-2.19210.23962340.20514640100
2.1921-2.24310.24792110.2074757100
2.2431-2.29920.25972620.19374702100
2.2992-2.36140.22442310.19454682100
2.3614-2.43090.20712770.18894642100
2.4309-2.50930.23842560.18624710100
2.5093-2.5990.2152680.17894673100
2.599-2.70310.18232190.17344734100
2.7031-2.82610.22742100.17594735100
2.8261-2.97510.23472580.17454670100
2.9751-3.16150.1872470.17274726100
3.1615-3.40560.21952490.16134669100
3.4056-3.74830.19912390.1644691100
3.7483-4.29050.17022100.1454728100
4.2905-5.40520.1562540.14264697100
5.4052-65.4750.20222300.19384712100
Refinement TLS params.Method: refined / Origin x: 72.0985 Å / Origin y: 47.504 Å / Origin z: 11.2288 Å
111213212223313233
T0.1985 Å20.0027 Å20.0072 Å2-0.1852 Å20.0152 Å2--0.1924 Å2
L0.7301 °20.1556 °2-0.3682 °2-0.2459 °2-0.2222 °2--0.8802 °2
S-0.0918 Å °-0.0264 Å °-0.1477 Å °-0.0927 Å °0.0374 Å °-0.0606 Å °0.2148 Å °0.0144 Å °0.0433 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA388 - 615
2X-RAY DIFFRACTION1allA701 - 1301
3X-RAY DIFFRACTION1allB388 - 616
4X-RAY DIFFRACTION1allB701 - 901
5X-RAY DIFFRACTION1allC1 - 4
6X-RAY DIFFRACTION1allS1 - 420

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