8GYN

zebrafish TIPE1 strucutre in complex with PE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural insight into TIPE1 functioning as a lipid transfer protein.

Cao, S.Zhang, Y.Jiang, H.Hou, X.Wang, W.

(2023) J Biomol Struct Dyn 41: 14049-14062

  • DOI: https://doi.org/10.1080/07391102.2023.2187641
  • Primary Citation of Related Structures:  
    8GYN

  • PubMed Abstract: 

    As a member of the tumor necrosis factor-α-induced protein 8 (TNFAIP8/TIPE) family, TIPE1 has been found to be associated with many cellular signaling pathways in regulating apoptosis, autophagy, and tumorigenesis. However, the position of TIPE1 in the signaling network remains elusive. Here we present the crystal structure of zebrafish TIPE1 in complex with phosphatidylethanolamine (PE) at a resolution of 1.38 Å. By comparison with structures of other three TIPE family proteins, a universal phospholipid-binding mode was proposed. Namely, the hydrophobic cavity binds to fatty acid tails, while 'X-R-R' triad nearby the entrance of cavity recognizes the phosphate group head. Using molecular dynamics (MD) simulations, we further elaborated the mechanism of how the lysine-rich N-terminal domain assisting TIPE1 to favorably bind to phosphatidylinositol (PI). Beside small molecule substrate, we identified Gαi3 as a direct-binding partner of TIPE1 using GST pull-down assay and size-exclusion chromatography. Analyses of key-residue mutations and predicted complex structure revealed that the binding mode of TIPE1 to Gαi3 could be non-canonical. In summary, our findings narrowed down TIPE1's position in Gαi3-related and PI-inducing signaling pathways.Communicated by Ramaswamy H. Sarma.


  • Organizational Affiliation

    Advanced Medical Research Institute, Interventional Medicine Department, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor alpha-induced protein 8-like protein 1160Danio rerioMutation(s): 0 
Gene Names: tnfaip8l1tnfaip8si:dkey-49m19.6zgc:55331
UniProt
Find proteins for Q7SZE8 (Danio rerio)
Explore Q7SZE8 
Go to UniProtKB:  Q7SZE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7SZE8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6OU (Subject of Investigation/LOI)
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: 1.38 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.08α = 90
b = 65.92β = 106.55
c = 35.49γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171207
National Natural Science Foundation of China (NSFC)China31970584

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-20
    Changes: Database references