1K8R

Crystal structure of Ras-Bry2RBD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Ras-Byr2RBD complex: structural basis for Ras effector recognition in yeast.

Scheffzek, K.Grunewald, P.Wohlgemuth, S.Kabsch, W.Tu, H.Wigler, M.Wittinghofer, A.Herrmann, C.

(2001) Structure 9: 1043-1050

  • DOI: https://doi.org/10.1016/s0969-2126(01)00674-8
  • Primary Citation of Related Structures:  
    1K8R

  • PubMed Abstract: 

    The small GTP binding protein Ras has important roles in cellular growth and differentiation. Mutant Ras is permanently active and contributes to cancer development. In its activated form, Ras interacts with effector proteins, frequently initiating a kinase cascade. In the lower eukaryotic Schizosaccharomyces pombe, Byr2 kinase represents a Ras target that in terms of signal-transduction hierarchy can be considered a homolog of mammalian Raf-kinase. The activation mechanism of protein kinases by Ras is not understood, and there is no detailed structural information about Ras binding domains (RBDs) in nonmammalian organisms. The crystal structure of the Ras-Byr2RBD complex at 3 A resolution shows a complex architecture similar to that observed in mammalian homologous systems, with an interprotein beta sheet stabilized by predominantly polar interactions between the interacting components. The C-terminal half of the Ras switch I region contains most of the contact anchors, while on the Byr2 side, a number of residues from topologically distinct regions are involved in complex stabilization. A C-terminal helical segment, which is not present in the known mammalian homologous systems and which is part of the auto-inhibitory region, has an additional binding site outside the switch I region. The structure of the Ras-Byr2 complex confirms the Ras binding module as a communication element mediating Ras-effector interactions; the Ras-Byr2 complex is also conserved in a lower eukaryotic system like yeast, which is in contrast to other small GTPase families. The extra helical segment might be involved in kinase activation.


  • Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abt. Strukturelle Biologie, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming protein P21/H-RAS-1166Homo sapiensMutation(s): 0 
Gene Names: Hras or Hras1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein kinase byr2110Schizosaccharomyces pombeMutation(s): 0 
Gene Names: BYR2 or STE8 or SPBC1D7.05
EC: 2.7.1 (PDB Primary Data), 2.7.11.25 (UniProt)
UniProt
Find proteins for P28829 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P28829 
Go to UniProtKB:  P28829
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28829
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.03α = 90
b = 139.03β = 90
c = 112.8γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
X-GENdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description