7U4Q | pdb_00007u4q

Human Synaptotagmin-1 C2A Y181F Ca2+ bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The AD3 locus of synaptotagmin-1 C2 domains modulates domain stability.

Dominguez, M.J.Bui, A.A.Villarreal, J.Snow, A.Karmakar, S.Harsini, F.M.Rock, P.J.Rice, A.M.Fuson, K.L.Sutton, R.B.

(2024) Biophys J 

  • DOI: https://doi.org/10.1016/j.bpj.2024.11.009
  • Primary Citation of Related Structures:  
    4WEE, 7TUA, 7TX9, 7U4Q

  • PubMed Abstract: 

    Synaptotagmin-1 (syt1) functions as the Ca 2+ -dependent sensor that triggers the rapid and synchronous release of neurotransmitters from neurotransmitter-containing vesicles during neuronal exocytosis. The syt1 protein has two homologous tandem C2 domains that interact with phospholipids in a Ca 2+ -dependent manner. Despite the crucial role of syt1 in exocytosis, the precise interactions between Ca 2+ , syt1, and phospholipids are not fully understood. In a study involving recessive lethal mutations in the syt1 gene, a specific mutation named AD3 was generated in Drosophila syt1, resulting in a significant reduction in Ca 2+ -dependent exocytosis. Further investigation revealed that the AD3 mutation was a missense mutation located in a conserved consensus sequence within the C2B domain of Drosophila syt1. However, the biophysical impact of the AD3 mutation had not been analyzed. Our study uses x-ray crystallography, isothermal titration calorimetry, thermodynamic analysis, and molecular dynamics simulation to show that the primary defect caused by the AD3 mutation in the syt1 protein is reduced thermodynamic stability. This instability alters the population of Ca 2+ -receptive states, leading to two major consequences: decreased affinity for calcium ions and compromised stabilization of the domain normally enhanced by Ca 2+ . We conclude that this conserved residue acts as a structural constraint, delimiting the movement of loop 3 within the pocket and ultimately influencing the affinity of the calcium ion binding with the C2 domain.


  • Organizational Affiliation

    Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, Texas.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin-1
A, B
133Homo sapiensMutation(s): 1 
Gene Names: SYT1SVP65SYT
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P21579 (Homo sapiens)
Explore P21579 
Go to UniProtKB:  P21579
PHAROS:  P21579
GTEx:  ENSG00000067715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21579
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.81α = 90
b = 99.81β = 90
c = 77.31γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
xia2data reduction
xia2data scaling
BUCCANEERmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United States1R21MH070589-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2025-01-15
    Changes: Database references, Structure summary