8FAM

Edited Octopus bimaculoides Synaptotagmin 1 C2A (I248V) at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Temperature-dependent RNA editing in octopus extensively recodes the neural proteome.

Birk, M.A.Liscovitch-Brauer, N.Dominguez, M.J.McNeme, S.Yue, Y.Hoff, J.D.Twersky, I.Verhey, K.J.Sutton, R.B.Eisenberg, E.Rosenthal, J.J.C.

(2023) Cell 186: 2544-2555.e13

  • DOI: https://doi.org/10.1016/j.cell.2023.05.004
  • Primary Citation of Related Structures:  
    8FAF, 8FAM

  • PubMed Abstract: 

    In poikilotherms, temperature changes challenge the integration of physiological function. Within the complex nervous systems of the behaviorally sophisticated coleoid cephalopods, these problems are substantial. RNA editing by adenosine deamination is a well-positioned mechanism for environmental acclimation. We report that the neural proteome of Octopus bimaculoides undergoes massive reconfigurations via RNA editing following a temperature challenge. Over 13,000 codons are affected, and many alter proteins that are vital for neural processes. For two highly temperature-sensitive examples, recoding tunes protein function. For synaptotagmin, a key component of Ca 2+ -dependent neurotransmitter release, crystal structures and supporting experiments show that editing alters Ca 2+ binding. For kinesin-1, a motor protein driving axonal transport, editing regulates transport velocity down microtubules. Seasonal sampling of wild-caught specimens indicates that temperature-dependent editing occurs in the field as well. These data show that A-to-I editing tunes neurophysiological function in response to temperature in octopus and most likely other coleoids.


  • Organizational Affiliation

    Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Biology, Saint Francis University, Loretto, PA 15940, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Synaptotagmin
A, B
131Octopus bimaculoidesMutation(s): 1 
Gene Names: OCBIM_22021175mg
UniProt
Find proteins for A0A0L8IHK9 (Octopus bimaculoides)
Explore A0A0L8IHK9 
Go to UniProtKB:  A0A0L8IHK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0L8IHK9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.924α = 90
b = 49.422β = 106.28
c = 71.706γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection