5KJ8

Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form) - from synchrotron diffraction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.

Lyubimov, A.Y.Uervirojnangkoorn, M.Zeldin, O.B.Zhou, Q.Zhao, M.Brewster, A.S.Michels-Clark, T.Holton, J.M.Sauter, N.K.Weis, W.I.Brunger, A.T.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.18740
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce a ...

    X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models.


    Organizational Affiliation

    Neurology and Neurological Science, Stanford University, Stanford, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vesicle-associated membrane protein 3
A, G
63Rattus norvegicusMutation(s): 0 
Gene Names: Vamp3 (Syb3)
Find proteins for P63025 (Rattus norvegicus)
Go to UniProtKB:  P63025
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Syntaxin-1A
B, H
66Rattus norvegicusMutation(s): 0 
Gene Names: Stx1a (Sap)
Find proteins for P32851 (Rattus norvegicus)
Go to UniProtKB:  P32851
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 25
C, I
75Rattus norvegicusMutation(s): 0 
Gene Names: Snap25 (Snap)
Find proteins for P60881 (Rattus norvegicus)
Go to UniProtKB:  P60881
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Synaptosomal-associated protein 25
D, J
64Rattus norvegicusMutation(s): 0 
Gene Names: Snap25 (Snap)
Find proteins for P60881 (Rattus norvegicus)
Go to UniProtKB:  P60881
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Synaptotagmin-1
E, F, K
279Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Find proteins for P21707 (Rattus norvegicus)
Go to UniProtKB:  P21707
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
C, E, F, K
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.1 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.283 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.790α = 90.00
b = 169.710β = 90.00
c = 286.790γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references