Zinc finger domain of the human DTX protein

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2018-11-09 Released: 2019-11-13 
  • Deposition Author(s): Miyamoto, K.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Zinc finger domain of the human DTX protein adopts a unique RING fold.

Miyamoto, K.Fujiwara, Y.Saito, K.

(2019) Protein Sci 28: 1151-1156

  • DOI: https://doi.org/10.1002/pro.3610
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Deltex (DTX) family is involved in ubiquitination and acts as Notch signaling modifiers for controlling cell fate determination. DTX promotes the development of the ubiquitin chain via its RING finger (DTX_RING). In this study, the solution structure of DTX_RING was determined using nuclear magnetic resonance (NMR). Moreover, by experiments with a metallochromic indicator, we spectrophotometrically estimated the stoichiometry of zinc ions and found that DTX_RING possesses zinc-binding capabilities. The Simple Modular Architecture Research Tool database predicted the structure of DTX_RING as a typical RING finger. However, the actual DTX_RING structure adopts a novel RING fold with a unique topology distinct from other RING fingers. We unveiled the position and the range of the DTX_RING active site at the atomic level. Artificial RING fingers (ARFs) are made by grafting active sites of the RING fingers onto cross-brace structure motifs. Therefore, the present structural analysis could be useful for designing a novel ARF.

  • Organizational Affiliation

    Department of Pharmaceutical Health Care, Faculty of Pharmaceutical Sciences, Himeji Dokkyo University, Himeji, Hyogo, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable E3 ubiquitin-protein ligase DTX276Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q86UW9 (Homo sapiens)
Explore Q86UW9 
Go to UniProtKB:  Q86UW9
GTEx:  ENSG00000091073 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86UW9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2019-11-13 
  • Deposition Author(s): Miyamoto, K.

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references