5VFF | pdb_00005vff

Synaptotagmin 1 C2B domain, lead-bound (low occupancy)

• PDB DOI: https://doi.org/10.2210/pdb5VFF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-04-07 Released: 2018-04-11 
• Deposition Author(s): Taylor, A.B., Hart, P.J., Igumenova, T.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

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

• PubMed: 30063057 
• DOI: https://doi.org/10.1039/c8mt00135a
• Primary Citation Related Structures: 
  5VFE, 5VFF, 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. 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.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Boulevard, College Station, TX 77843, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.42 kDa 
• Atom Count: 1,477 
• Modeled Residue Count: 149 
• Deposited Residue Count: 151 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Synaptotagmin-1	A	151	Mus musculus	Mutation(s): 1  Gene Names: Syt1
UniProt & NIH Common Fund Data Resources
Find proteins for P46096 (Mus musculus) Explore P46096  Go to UniProtKB:  P46096
IMPC:  MGI:99667

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PB	B [auth A]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.634	α = 90
b = 41.117	β = 90
c = 82.854	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Taylor, A.B., Hart, P.J., Igumenova, T.I.

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description