5KJ8

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

Summary for 5KJ8

• Entry DOI: 10.2210/pdb5kj8/pdb
• Related: 5KJ7
• Descriptor: Vesicle-associated membrane protein 3, Syntaxin-1A, Synaptosomal-associated protein 25, ... (6 entities in total)
• Functional Keywords: xfel structure, synaptic fusion complex, synaptotagmin1, neuronal snare complex, endocytosis, exocytosis
• Biological source: Rattus norvegicus (Rat); More
• Cellular location: Membrane ; Single-pass type IV membrane protein : P63025; Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane ; Single-pass type IV membrane protein : P32851; Cytoplasm, perinuclear region : P60881 P60881; Cytoplasmic vesicle, secretory vesicle membrane ; Single-pass membrane protein : P21707
• Total number of polymer chains: 11
• Total formula weight: 158567.05

Authors

Lyubimov, A.Y.,Uervirojnangkoorn, M.,Zhou, Q.,Zhao, M.,Sauter, N.K.,Brewster, A.S.,Weis, W.I.,Brunger, A.T. (deposition date: 2016-06-17, release date: 2016-10-19, Last modification date: 2023-09-27)

Primary citation

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.
Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex.
Elife, 5:-, 2016

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 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.

PubMed: 27731796
DOI: 10.7554/eLife.18740

Experimental method

X-RAY DIFFRACTION (4.1 Å)