6TZ3

Crystal Structure of Human Synaptotagmin 1 C2B without Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular Basis for Synaptotagmin-1-Associated Neurodevelopmental Disorder.

Bradberry, M.M.Courtney, N.A.Dominguez, M.J.Lofquist, S.M.Knox, A.T.Sutton, R.B.Chapman, E.R.

(2020) Neuron 107: 52-64.e7

  • DOI: 10.1016/j.neuron.2020.04.003
  • Primary Citation of Related Structures:  
    6U41, 6U4U, 6U4W, 6TZ3

  • PubMed Abstract: 
  • At neuronal synapses, synaptotagmin-1 (syt1) acts as a Ca 2+ sensor that synchronizes neurotransmitter release with Ca 2+ influx during action potential firing. Heterozygous missense mutations in syt1 have recently been associated ...

    At neuronal synapses, synaptotagmin-1 (syt1) acts as a Ca 2+ sensor that synchronizes neurotransmitter release with Ca 2+ influx during action potential firing. Heterozygous missense mutations in syt1 have recently been associated with a severe but heterogeneous developmental syndrome, termed syt1-associated neurodevelopmental disorder. Well-defined pathogenic mechanisms, and the basis for phenotypic heterogeneity in this disorder, remain unknown. Here, we report the clinical, physiological, and biophysical characterization of three syt1 mutations from human patients. Synaptic transmission was impaired in neurons expressing mutant variants, which demonstrated potent, graded dominant-negative effects. Biophysical interrogation of the mutant variants revealed novel mechanistic features concerning the cooperative action, and functional specialization, of the tandem Ca 2+ -sensing domains of syt1. These mechanistic studies led to the discovery that a clinically approved K + channel antagonist is able to rescue the dominant-negative heterozygous phenotype. Our results establish a molecular cause, basis for phenotypic heterogeneity, and potential treatment approach for syt1-associated neurodevelopmental disorder.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA. Electronic address: chapman@wisc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptotagmin-1 A157Homo sapiensMutation(s): 0 
Gene Names: SYT1SVP65SYT
Find proteins for P21579 (Homo sapiens)
Explore P21579 
Go to UniProtKB:  P21579
NIH Common Fund Data Resources
PHAROS:  P21579
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.17 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.594α = 90
b = 54.594β = 90
c = 103.904γ = 120
Software Package:
Software NamePurpose
PDB-REDOrefinement
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references