6NYT

Munc13-1 C2B-domain, calcium bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3KWU


Literature

Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis.

Shin, O.H.Lu, J.Rhee, J.S.Tomchick, D.R.Pang, Z.P.Wojcik, S.M.Camacho-Perez, M.Brose, N.Machius, M.Rizo, J.Rosenmund, C.Sudhof, T.C.

(2010) Nat Struct Mol Biol 17: 280-288

  • DOI: https://doi.org/10.1038/nsmb.1758
  • Primary Citation of Related Structures:  
    6NYC, 6NYT

  • PubMed Abstract: 

    Munc13 is a multidomain protein present in presynaptic active zones that mediates the priming and plasticity of synaptic vesicle exocytosis, but the mechanisms involved remain unclear. Here we use biophysical, biochemical and electrophysiological approaches to show that the central C(2)B domain of Munc13 functions as a Ca(2+) regulator of short-term synaptic plasticity. The crystal structure of the C(2)B domain revealed an unusual Ca(2+)-binding site with an amphipathic alpha-helix. This configuration confers onto the C(2)B domain unique Ca(2+)-dependent phospholipid-binding properties that favor phosphatidylinositolphosphates. A mutation that inactivated Ca(2+)-dependent phospholipid binding to the C(2)B domain did not alter neurotransmitter release evoked by isolated action potentials, but it did depress release evoked by action-potential trains. In contrast, a mutation that increased Ca(2+)-dependent phosphatidylinositolbisphosphate binding to the C(2)B domain enhanced release evoked by isolated action potentials and by action-potential trains. Our data suggest that, during repeated action potentials, Ca(2+) and phosphatidylinositolphosphate binding to the Munc13 C(2)B domain potentiate synaptic vesicle exocytosis, thereby offsetting synaptic depression induced by vesicle depletion.


  • Organizational Affiliation

    Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein unc-13 homolog A148Rattus norvegicusMutation(s): 1 
Gene Names: Unc13aUnc13h1
UniProt
Find proteins for Q62768 (Rattus norvegicus)
Explore Q62768 
Go to UniProtKB:  Q62768
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62768
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.943α = 90
b = 56.943β = 90
c = 89.983γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
AMoREphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS40944
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS051262

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description