1UAD

Crystal structure of the RalA-GppNHp-Sec5 Ral-binding domain complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural basis of the interaction between RalA and Sec5, a subunit of the Sec6/8 complex

Fukai, S., Matern, H.T., Jagath, J.R., Scheller, R.H., Brunger, A.T.

(2003) EMBO J. 22: 3267-3278

  • DOI: 10.1093/emboj/cdg329

  • PubMed Abstract: 

    • The sec6/8 complex or exocyst is an octameric protein complex that functions during cell polarization by regulating the site of exocytic vesicle docking to the plasma membrane, in concert with small GTP-binding proteins. The Sec5 subunit of the mamma ...

    The sec6/8 complex or exocyst is an octameric protein complex that functions during cell polarization by regulating the site of exocytic vesicle docking to the plasma membrane, in concert with small GTP-binding proteins. The Sec5 subunit of the mammalian sec6/8 complex binds Ral in a GTP-dependent manner. Here we report the crystal structure of the complex between the Ral-binding domain of Sec5 and RalA bound to a non-hydrolyzable GTP analog (GppNHp) at 2.1 A resolution, providing the first structural insights into the mechanism and specificity of sec6/8 regulation. The Sec5 Ral-binding domain folds into an immunoglobulin-like beta-sandwich structure, which represents a novel fold for an effector of a GTP-binding protein. The interface between the two proteins involves a continuous antiparallel beta-sheet, similar to that found in other effector/G-protein complexes, such as Ras and Rap1A. Specific interactions unique to the RalA.Sec5 complex include Sec5 Thr11 and Arg27, and RalA Glu38, which we show are required for complex formation by isothermal titration calorimetry. Comparison of the structures of GppNHp- and GDP-bound RalA suggests a nucleotide-dependent switch mechanism for Sec5 binding.

    Organizational Affiliation: 

    Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, James H.Clark Center, E300C, 318 Campus Drive, Stanford, CA 94305-5432, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Ral-A
A, B
175Homo sapiensMutation(s): 0 
Gene Names: RALA (RAL)
Find proteins for P11233 (Homo sapiens)
Go to Gene View: RALA
Go to UniProtKB:  P11233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Exocyst complex component Sec5
C, D
99Rattus norvegicusMutation(s): 0 
Gene Names: Exoc2 (Sec5, Sec5l1)
Find proteins for O54921 (Rattus norvegicus)
Go to UniProtKB:  O54921
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GNPKa: 7260000 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 117.418α = 90.00
b = 117.418β = 90.00
c = 102.676γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance