2A2F | pdb_00002a2f

Crystal Structure of Sec15 C-terminal domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.276 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.244 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2A2F

This is version 1.3 of the entry. See complete history. 

Literature

Sec15 interacts with Rab11 via a novel domain and affects Rab11 localization in vivo.

Wu, S., Mehta, S.Q., Pichaud, F., Bellen, H.J., Quiocho, F.A.

(2005) Nat Struct Mol Biol 12: 879-885

  • DOI: https://doi.org/10.1038/nsmb987
  • Primary Citation Related Structures: 
    2A2F

  • PubMed Abstract: 

    Sec15, a component of the exocyst, recognizes vesicle-associated Rab GTPases, helps target transport vesicles to the budding sites in yeast and is thought to recruit other exocyst proteins. Here we report the characterization of a 35-kDa fragment that comprises most of the C-terminal half of Drosophila melanogaster Sec15. This C-terminal domain was found to bind a subset of Rab GTPases, especially Rab11, in a GTP-dependent manner. We also provide evidence that in fly photoreceptors Sec15 colocalizes with Rab11 and that loss of Sec15 affects rhabdomere morphology. Determination of the 2.5-A crystal structure of the C-terminal domain revealed a novel fold consisting of ten alpha-helices equally distributed between two subdomains (N and C subdomains). We show that the C subdomain, mainly via a single helix, is sufficient for Rab binding.

    • Organizational Affiliation: 
    • Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.

Macromolecule Content 

  • Total Structure Weight: 37.96 kDa 
  • Atom Count: 2,511 
  • Modeled Residue Count: 296 
  • Deposited Residue Count: 325 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Exocyst complex component Sec15A [auth X]325Drosophila melanogasterMutation(s): 0 
Gene Names: sec15
UniProt
Find proteins for Q9VDE6 (Drosophila melanogaster)
Explore Q9VDE6 
Go to UniProtKB:  Q9VDE6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VDE6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.276 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.244 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.5α = 90
b = 93.9β = 90
c = 123.5γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-09-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references