Solution structure of C2B with IP6

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Molecular Level Interaction of Inositol Hexaphosphate with the C2B Domain of Human Synaptotagmin I

Joung, M.Mohan, S.K.Yu, C.

(2012) Biochemistry 

  • DOI: https://doi.org/10.1021/bi300005w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Synaptotagmin I is a synaptic vesicle membrane protein that serves as a multifunctional regulator during the exocytosis of neurotransmitter release. It contains C2A and C2B domains. The binding of Ca(2+) to the C2A domain activates the exocytosis of secretory vesicles, while the binding of inositol polyphosphates (IP4-IP6) to the C2B domain inhibits this process. To understand the IP6-induced inhibition of exocytosis of secretory vesicles, we determined the three-dimensional structure of the C2B-IP6 complex by nuclear magnetic resonance (NMR). In this study, we have determined the binding constant by isothermal titration calorimetry. The circular dichroism measurements demonstrated that IP6 can stabilize the C2B molecule. We identified the binding site using (1)H-(15)N heteronuclear single-quantum coherence spectroscopy titration data and determined the structure of the C2B-IP6 complex using multidimensional NMR studies. This information will aid in the design of better pharmacological treatments for neurological disorders.

  • Organizational Affiliation

    Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin-1152Homo sapiensMutation(s): 0 
Gene Names: SYT1SVP65SYT
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens)
Explore P21579 
Go to UniProtKB:  P21579
GTEx:  ENSG00000067715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21579
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on IHP

Download Ideal Coordinates CCD File 
C6 H18 O24 P6
Binding Affinity Annotations 
IDSourceBinding Affinity
IHP PDBBind:  2LHA Kd: 6400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Non-polymer description
  • Version 1.2: 2020-10-14
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-06-14
    Changes: Database references, Other