5JXD | pdb_00005jxd

Crystal structure of murine Tnfaip8 C165S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.287 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

The Tnfaip8-PE complex is a novel upstream effector in the anti-autophagic action of insulin

Kim, J.S.Park, J.Kim, M.S.Ha, J.Y.Jang, Y.W.Shin, D.H.Son, J.H.

(2017) Sci Rep 7: 6248-6248

  • DOI: https://doi.org/10.1038/s41598-017-06576-3
  • Primary Citation Related Structures: 
    5JXD

  • PubMed Abstract: 

    Defective hepatic autophagy is observed in obesity and diabetes, whereas autophagy is inhibited by insulin in hepatocytes. Insulin-induced anti-autophagy is mediated by non-canonical Gαi3 signaling via an unknown mechanism. Previously, we identified the anti-autophagic activity of Tnfaip8 via activation of mammalian target of rapamycin (mTOR) in the nervous system. Here, we demonstrate that insulin temporally induces Tnfaip8, which mediates the anti-autophagic action of insulin through formation of a novel ternary complex including Tnfaip8, phosphatidylethanolamine (PE) and Gαi3. Specifically, an X-ray crystallographic study of Tnfaip8 from Mus musculus (mTnfaip8) at 2.03 Å together with LC-MS analyses reveals PE in the hydrophobic cavity. However, an mTnfaip8 mutant lacking PE does not interact with Gαi3, indicating that the PE component is critical for the anti-autophagic action of mTnfaip8 via interaction with Gαi3. Therefore, the mTnfaip8-PE complex may act as an essential upstream effector via ternary complex formation most likely with active Gαi3 during insulin-induced anti-autophagy.


  • Organizational Affiliation
    • College of Pharmacy and Graduate School of Pharmaceutical Sciences, Global Top5 Research Program, Ewha W. University, Seoul, 03760, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 23.7 kDa 
  • Atom Count: 1,589 
  • Modeled Residue Count: 186 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor alpha-induced protein 8198Mus musculusMutation(s): 1 
UniProt
Find proteins for Q921Z5 (Mus musculus)
Explore Q921Z5 
Go to UniProtKB:  Q921Z5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ921Z5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6OU

Query on 6OU



Download:Ideal Coordinates CCD File
B [auth A][(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
C39 H76 N O8 P
FHQVHHIBKUMWTI-OTMQOFQLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.287 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.276α = 90
b = 71.57β = 90
c = 90.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Science and TechnologyKorea, Republic Of2010K000266

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description