1UAD

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

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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
  • Primary Citation of Related Structures:  
    1UAD

  • 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 mammalian sec6/8 complex binds Ral in a GTP-dependent manner ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Ral-AA, B175Homo sapiensMutation(s): 0 
Gene Names: RALA, RAL
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P11233 (Homo sapiens)
Explore P11233 
Go to UniProtKB:  P11233
PHAROS:  P11233
GTEx:  ENSG00000006451 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11233
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exocyst complex component Sec5C, D99Rattus norvegicusMutation(s): 0 
Gene Names: Exoc2, Sec5, Sec5l1
UniProt
Find proteins for O54921 (Rattus norvegicus)
Explore O54921 
Go to UniProtKB:  O54921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO54921
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GNP Binding MOAD:  1UAD Ka: 7.26e+6 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.418α = 90
b = 117.418β = 90
c = 102.676γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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