5KJ7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 

wwPDB Validation   3D Report Full Report


This is version 1.6 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:  
    5KJ7, 5KJ8

  • 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 ...

    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

    Howard Hughes Medical Institute, Stanford University, Stanford, United States.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Vesicle-associated membrane protein 3 AG63Rattus norvegicusMutation(s): 0 
Gene Names: Vamp3Syb3
Find proteins for P63025 (Rattus norvegicus)
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Go to UniProtKB:  P63025
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Syntaxin-1A BH66Rattus norvegicusMutation(s): 0 
Gene Names: Stx1aSap
Find proteins for P32851 (Rattus norvegicus)
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Go to UniProtKB:  P32851
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptosomal-associated protein 25 CI75Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Find proteins for P60881 (Rattus norvegicus)
Explore P60881 
Go to UniProtKB:  P60881
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptosomal-associated protein 25 DJ64Rattus norvegicusMutation(s): 0 
Gene Names: Snap25Snap
Find proteins for P60881 (Rattus norvegicus)
Explore P60881 
Go to UniProtKB:  P60881
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Synaptotagmin-1 EFK279Rattus norvegicusMutation(s): 0 
Gene Names: Syt1
Find proteins for P21707 (Rattus norvegicus)
Explore P21707 
Go to UniProtKB:  P21707
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.294 
  • Space Group: P 21 21 21
  • Diffraction Data DOI: 10.15785/SBGRID/365 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.386α = 90
b = 170.676β = 90
c = 291.014γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
cctbx.primedata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hughes Collaborative Innovation AwardUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM102520
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM117126

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2018-02-14
    Changes: Data collection
  • Version 1.5: 2018-11-28
    Changes: Data collection
  • Version 1.6: 2019-12-25
    Changes: Author supporting evidence