1XD2

Crystal Structure of a ternary Ras:SOS:Ras*GDP complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


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


Literature

Structural analysis of autoinhibition in the ras activator son of sevenless.

Sondermann, H., Soisson, S.M., Boykevisch, S., Yang, S.S., Bar-Sagi, D., Kuriyan, J.

(2004) Cell 119: 393-405

  • DOI: 10.1016/j.cell.2004.10.005
  • Primary Citation of Related Structures:  
    1XD4, 1XD2, 1XDV

  • PubMed Abstract: 

    • The classical model for the activation of the nucleotide exchange factor Son of sevenless (SOS) involves its recruitment to the membrane, where it engages Ras. The recent discovery that Ras*GTP is an allosteric activator of SOS indicated that the regulat ...

    The classical model for the activation of the nucleotide exchange factor Son of sevenless (SOS) involves its recruitment to the membrane, where it engages Ras. The recent discovery that Ras*GTP is an allosteric activator of SOS indicated that the regulation of SOS is more complex than originally envisaged. We now present crystallographic and biochemical analyses of a construct of SOS that contains the Dbl homology-pleckstrin homology (DH-PH) and catalytic domains and show that the DH-PH unit blocks the allosteric binding site for Ras and suppresses the activity of SOS. SOS is dependent on Ras binding to the allosteric site for both a lower level of activity, which is a result of Ras*GDP binding, and maximal activity, which requires Ras*GTP. The action of the DH-PH unit gates a reciprocal interaction between Ras and SOS, in which Ras converts SOS from low to high activity forms as Ras*GDP is converted to Ras*GTP by SOS.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, Department of Molecular and Cell Biology and Department of Chemistry, University of California, Berkeley, CA 94720, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transforming protein p21/H-Ras-1 A166Homo sapiensMutation(s): 1 
Gene Names: HRAS, HRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112
GTEx:  ENSG00000174775
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transforming protein p21/H-Ras-1 B166Homo sapiensMutation(s): 0 
Gene Names: HRAS, HRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112
GTEx:  ENSG00000174775
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Son of sevenless protein homolog 1 C484Homo sapiensMutation(s): 0 
Gene Names: SOS1
Find proteins for Q07889 (Homo sapiens)
Explore Q07889 
Go to UniProtKB:  Q07889
NIH Common Fund Data Resources
PHAROS:  Q07889
GTEx:  ENSG00000115904
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.703α = 90
b = 183.703β = 90
c = 177.804γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance