5VFE

Synaptotagmin 1 C2A domain, lead-bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

High affinity interactions of Pb2+with synaptotagmin I.

Katti, S., Her, B., Srivastava, A.K., Taylor, A.B., Lockless, S.W., Igumenova, T.I.

(2018) Metallomics 10: 1211-1222

  • DOI: 10.1039/c8mt00135a
  • Primary Citation of Related Structures:  
    5VFF, 5VFE, 5VFG

  • PubMed Abstract: 

    • Lead (Pb) is a potent neurotoxin that disrupts synaptic neurotransmission. We report that Synaptotagmin I (SytI), a key regulator of Ca2+-evoked neurotransmitter release, has two high-affinity Pb2+ binding sites that belong to its cytosolic C2A and C2B domains ...

    Lead (Pb) is a potent neurotoxin that disrupts synaptic neurotransmission. We report that Synaptotagmin I (SytI), a key regulator of Ca2+-evoked neurotransmitter release, has two high-affinity Pb2+ binding sites that belong to its cytosolic C2A and C2B domains. The crystal structures of Pb2+-complexed C2 domains revealed that protein-bound Pb2+ ions have holodirected coordination geometries and all-oxygen coordination spheres. The on-rate constants of Pb2+ binding to the C2 domains of SytI are comparable to those of Ca2+ and are diffusion-limited. In contrast, the off-rate constants are at least two orders of magnitude smaller, indicating that Pb2+ can serve as both a thermodynamic and kinetic trap for the C2 domains. We demonstrate, using NMR spectroscopy, that population of these sites by Pb2+ ions inhibits further Ca2+ binding despite the existing coordination vacancies. Our work offers a unique insight into the bioinorganic chemistry of Pb(ii) and suggests a mechanism by which low concentrations of Pb2+ ions can interfere with the Ca2+-dependent function of SytI in the cell.

    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA. tigumenova@tamu.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptotagmin-1 A, B126Mus musculusMutation(s): 0 
Gene Names: Syt1
Find proteins for P46096 (Mus musculus)
Explore P46096 
Go to UniProtKB:  P46096
NIH Common Fund Data Resources
IMPC:  MGI:99667
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB
Query on PB
Download Ideal Coordinates CCD File 
A, B
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.04α = 90
b = 55.04β = 90
c = 77.16γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references