8AY2

Crystal structure of the C-terminal part of rat Sec8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Sec8 specifically interacts with the PDZ2 domain of synapse associated protein 102 (SAP102).

Korbula, K.Hammerschmid, I.Lesigang, J.Dong, G.

(2023) Front Cell Dev Biol 11: 1254611-1254611

  • DOI: https://doi.org/10.3389/fcell.2023.1254611
  • Primary Citation of Related Structures:  
    8AY2

  • PubMed Abstract: 

    The exocyst is an evolutionarily conserved protein complex tethering secretory vesicles before their docking and fusion with the plasma membrane. The complex also plays important roles in cell migration, synaptogenesis, and neurite outgrowth. One of its subunits, Sec8, was reported to interact with two major synaptic scaffolding proteins SAP102 and PSD-95 that share high sequence homology and contain three PDZ domains at their N-terminal region. The interaction is via the binding of the C-terminal ITTV motif in Sec8 to the PDZ domains of the two synaptic proteins. However, it remains elusive to which PDZ domain(s) Sec8 binds and how their interaction occurs. Here we reported a 2.5 Å resolution crystal structure of the C-terminal half of rat Sec8 containing the ITTV motif. The structure shows that Sec8 contains an enormously long helix at its C-terminus, which bears a unique long "spacer" of 14 residues to bridge the ITTV motif to the compact core of Sec8. We found that Sec8 preferentially binds PDZ2 over PDZ1 and PDZ3 of SAP102. Deletion of the spacer completely abolished the binding of Sec8 to SAP102. Overall, our structural studies, biochemical data and modeling analyses altogether provide an explanation for how Sec8 interacts with SAP102.


  • Organizational Affiliation

    Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exocyst complex component 4
A, B
424Rattus norvegicusMutation(s): 0 
Gene Names: Exoc4Sec8Sec8l1
UniProt
Find proteins for Q62824 (Rattus norvegicus)
Explore Q62824 
Go to UniProtKB:  Q62824
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62824
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.004α = 90
b = 190.004β = 90
c = 175.275γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaI5960-B2

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Database references