5ZI6 | pdb_00005zi6

The RING domain structure of MEX-3C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.243 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5ZI6

This is version 1.2 of the entry. See complete history

Literature

Structural and functional characterization of hMEX-3C Ring finger domain as an E3 ubiquitin ligase

Moududee, S.A.Jiang, Y.Gilbert, N.Xie, G.Xu, Z.Wu, J.Gong, Q.Tang, Y.Shi, Y.

(2018) Protein Sci 27: 1661-1669

  • DOI: https://doi.org/10.1002/pro.3473
  • Primary Citation Related Structures: 
    5ZI6

  • PubMed Abstract: 

    MEX-3C, a novel RNA binding E3 ubiquitin ligases, contains two N-terminal heterogeneous nuclear ribonucleoprotein K homology (KH) domains and C-terminal Ring finger domain. Recent evidence has suggested that human MEX-3C has a strong bondage with carcinogenesis and the MEX-3C-mediated ubiquitination of RIG-I is essential for the antiviral innate immune response. Moreover, the Ring finger domain of MEX-3C could regulate the degradation of HLA-A2 (an MHC-I allotype) mRNA with a novel mechanism. However, the structural basis for the ubiquitination catalyzed by hMEX-3C Ring finger domain remains evasive. In this study, we solved the crystal structure of dimeric Ring finger domain of hMEX-3C and compared it with the complex structure of MDM2/MDMX-UbcH5b-Ub. Our ubiquitination assay demonstrated that the Ring finger domain of hMEX-3C acts as a ubiquitin E3 ligase in vitro, cooperating with specific E2 to mediate ubiquitination. Then, we identified several key residues in Ring finger domain of hMEX-3C possibly involved in the interaction with E2-Ub conjugate and analyzed the E3 ligase activities of wild type and mutants at key sites. Additionally, zinc chelation experiments indicated that the intact structural stability is essential for the self-ubiquitination activity of the Ring finger domain of hMEX-3C. Taken together, our studies provided new insight into the mechanism of the Ring finger domain of hMEX-3C that may play an important role in eliciting antiviral immune responses and therapeutic interventions.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 49.49 kDa 
  • Atom Count: 3,346 
  • Modeled Residue Count: 440 
  • Deposited Residue Count: 440 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-binding E3 ubiquitin-protein ligase MEX3C
A, B, C, D, E
A, B, C, D, E, F, G, H
55Homo sapiensMutation(s): 0 
Gene Names: MEX3C
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q5U5Q3 (Homo sapiens)
Explore Q5U5Q3 
Go to UniProtKB:  Q5U5Q3
PHAROS:  Q5U5Q3
GTEx:  ENSG00000176624 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5U5Q3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth C]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth G],
W [auth H],
X [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.243 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.135α = 92.43
b = 44.567β = 90.5
c = 67.157γ = 91.39
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
SHELXCDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Refinement description