6MTI

Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins (5CCI) individually docked into Cryo-EM map of C2AB-SNARE complexes helically organized on lipid nanotube surface in presence of Mg2+


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the clamping and Ca2+activation of SNARE-mediated fusion by synaptotagmin.

Grushin, K.Wang, J.Coleman, J.Rothman, J.E.Sindelar, C.V.Krishnakumar, S.S.

(2019) Nat Commun 10: 2413-2413

  • DOI: 10.1038/s41467-019-10391-x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Synapotagmin-1 (Syt1) interacts with both SNARE proteins and lipid membranes to synchronize neurotransmitter release to calcium (Ca 2+ ) influx. Here we report the cryo-electron microscopy structure of the Syt1-SNARE complex on anionic-lip ...

    Synapotagmin-1 (Syt1) interacts with both SNARE proteins and lipid membranes to synchronize neurotransmitter release to calcium (Ca 2+ ) influx. Here we report the cryo-electron microscopy structure of the Syt1-SNARE complex on anionic-lipid containing membranes. Under resting conditions, the Syt1 C2 domains bind the membrane with a magnesium (Mg 2+ )-mediated partial insertion of the aliphatic loops, alongside weak interactions with the anionic lipid headgroups. The C2B domain concurrently interacts the SNARE bundle via the 'primary' interface and is positioned between the SNAREpins and the membrane. In this configuration, Syt1 is projected to sterically delay the complete assembly of the associated SNAREpins and thus, contribute to clamping fusion. This Syt1-SNARE organization is disrupted upon Ca 2+ -influx as Syt1 reorients into the membrane, likely displacing the attached SNAREpins and reversing the fusion clamp. We thus conclude that the cation (Mg 2+ /Ca 2+ ) dependent membrane interaction is a key determinant of the dual clamp/activator function of Synaptotagmin-1.


    Organizational Affiliation

    Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, Queens Square House, London, WC1 3BG, UK. shyam.krishnakumar@yale.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Synaptotagmin-1
1, 6
127Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
SNARE Protein Family
Protein: 
Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins
Find proteins for P21707 (Rattus norvegicus)
Go to UniProtKB:  P21707

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Synaptotagmin-1
2, 3, 4, 5
281Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
SNARE Protein Family
Protein: 
Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins
Find proteins for P21707 (Rattus norvegicus)
Go to UniProtKB:  P21707

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vesicle-associated membrane protein 2
A, E, I, M, Q, U
63Rattus norvegicusMutation(s): 0 
Gene Names: Vamp2Syb2
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
SNARE Protein Family
Protein: 
Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins
Find proteins for P63045 (Rattus norvegicus)
Go to UniProtKB:  P63045

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Syntaxin-1A
B, F, J, N, R, V
67Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
SNARE Protein Family
Protein: 
Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins
Find proteins for P32851 (Rattus norvegicus)
Go to UniProtKB:  P32851

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 25
C, G, K, O, S, W
77Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
SNARE Protein Family
Protein: 
Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins
Find proteins for P60881 (Rattus norvegicus)
Go to UniProtKB:  P60881

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 25
D, H, L, P, T, X
65Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
SNARE Protein Family
Protein: 
Synaptotagmin-1 C2A, C2B domains and SNARE-pin proteins
Find proteins for P60881 (Rattus norvegicus)
Go to UniProtKB:  P60881
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
1, 2, 3, 4, 5, 6
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK027044

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence