6LCY

Crystal structure of Synaptotagmin-7 C2B in complex with IP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

5-IP 7 is a GPCR messenger mediating neural control of synaptotagmin-dependent insulin exocytosis and glucose homeostasis.

Zhang, X.Li, N.Zhang, J.Zhang, Y.Yang, X.Luo, Y.Zhang, B.Xu, Z.Zhu, Z.Yang, X.Yan, Y.Lin, B.Wang, S.Chen, D.Ye, C.Ding, Y.Lou, M.Wu, Q.Hou, Z.Zhang, K.Liang, Z.Wei, A.Wang, B.Wang, C.Jiang, N.Zhang, W.Xiao, G.Ma, C.Ren, Y.Qi, X.Han, W.Wang, C.Rao, F.

(2021) Nat Metab 3: 1400-1414

  • DOI: https://doi.org/10.1038/s42255-021-00468-7
  • Primary Citation of Related Structures:  
    6LCY

  • PubMed Abstract: 

    5-diphosphoinositol pentakisphosphate (5-IP 7 ) is a signalling metabolite linked to various cellular processes. How extracellular stimuli elicit 5-IP 7 signalling remains unclear. Here we show that 5-IP 7 in β cells mediates parasympathetic stimulation of synaptotagmin-7 (Syt7)-dependent insulin release. Mechanistically, vagal stimulation and activation of muscarinic acetylcholine receptors triggers G αq -PLC-PKC-PKD-dependent signalling and activates IP6K1, the 5-IP 7 synthase. Whereas both 5-IP 7 and its precursor IP 6 compete with PIP 2 for binding to Syt7, Ca 2+ selectively binds 5-IP 7 with high affinity, freeing Syt7 to enable fusion of insulin-containing vesicles with the cell membrane. β-cell-specific IP6K1 deletion diminishes insulin secretion and glucose clearance elicited by muscarinic stimulation, whereas mice carrying a phosphorylation-mimicking, hyperactive IP6K1 mutant display augmented insulin release, congenital hyperinsulinaemia and obesity. These phenotypes are absent in mice lacking Syt7. Our study proposes a new conceptual framework for inositol pyrophosphate physiology in which 5-IP 7 acts as a GPCR second messenger at the interface between peripheral nervous system and metabolic organs, transmitting G q -coupled GPCR stimulation to unclamp Syt7-dependent, and perhaps other, exocytotic events.


  • Organizational Affiliation

    School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin-7145Mus musculusMutation(s): 0 
Gene Names: Syt7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9R0N7 (Mus musculus)
Explore Q9R0N7 
Go to UniProtKB:  Q9R0N7
IMPC:  MGI:1859545
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9R0N7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.406α = 90
b = 104.406β = 90
c = 53.404γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description