6Y5P | pdb_00006y5p

RING-DTC domain of Deltex1 bound to NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6Y5P

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases.

Chatrin, C.Gabrielsen, M.Buetow, L.Nakasone, M.A.Ahmed, S.F.Sumpton, D.Sibbet, G.J.Smith, B.O.Huang, D.T.

(2020) Sci Adv 6

  • DOI: https://doi.org/10.1126/sciadv.abc0418
  • Primary Citation Related Structures: 
    6Y5N, 6Y5P

  • PubMed Abstract: 

    Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin's Gly 76 Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD + Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD + bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.


  • Organizational Affiliation
    • Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.

Macromolecule Content 

  • Total Structure Weight: 54.22 kDa 
  • Atom Count: 4,143 
  • Modeled Residue Count: 457 
  • Deposited Residue Count: 470 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase DTX1
A, B
235Homo sapiensMutation(s): 0 
Gene Names: DTX1
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q86Y01 (Homo sapiens)
Explore Q86Y01 
Go to UniProtKB:  Q86Y01
PHAROS:  Q86Y01
GTEx:  ENSG00000135144 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86Y01
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
(Subject of Investigation/LOI)

Query on NAD



Download:Ideal Coordinates CCD File
C [auth A],
L [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
O [auth B],
P [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.85α = 90
b = 85.254β = 90
c = 130.949γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomA23278
European Research Council (ERC)United Kingdom647849

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary