1C1Y

CRYSTAL STRUCTURE OF RAP.GMPPNP IN COMPLEX WITH THE RAS-BINDING-DOMAIN OF C-RAF1 KINASE (RAFRBD).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue.

Nassar, N.

(1995) Nature 375: 554-560

  • DOI: 10.1038/375554a0
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The X-ray crystal structure of the complex between the Ras-related protein Rap1A in the GTP-analogue (GppNHp) form and the Ras-binding domain (RBD) of the Ras effector molecule c-Raf1, a Ser/Thr-specific protein kinase, has been solved to a resolutio ...

    The X-ray crystal structure of the complex between the Ras-related protein Rap1A in the GTP-analogue (GppNHp) form and the Ras-binding domain (RBD) of the Ras effector molecule c-Raf1, a Ser/Thr-specific protein kinase, has been solved to a resolution of 2.2 A. It shows that RBD has the ubiquitin superfold and that the structure of Rap1A is very similar to that of Ras. The interaction between the two proteins is mediated by an apparent central antiparallel beta-sheet formed by strands B1-B2 from RBD and strands beta 2-beta 3 from Rap1A. Complex formation is mediated by main-chain and side-chain interactions of the so-called effector residues in the switch I region of Rap1A.


    Related Citations: 
    • Ras/Rap effector specificty determined by charge reversal.
      Nassar, N.
      (1996) Nat Struct Biol 3: 723
    • Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B.
      Rehmann, H., Arias-Palomo, E., Hadders, M.A., Schwede, F., Llorca, O., Bos, J.L.
      (2008) Nature 455: 124

    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abteilung Strukturelle Biologie, Dortmund, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAS-RELATED PROTEIN RAP-1AA167Homo sapiensMutation(s): 0 
Gene Names: RAP1AKREV1
Find proteins for P62834 (Homo sapiens)
Explore P62834 
Go to UniProtKB:  P62834
NIH Common Fund Data Resources
PHAROS  P62834
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTO-ONCOGENE SERINE/THREONINE PROTEIN KINASE RAF-1B77Homo sapiensMutation(s): 0 
Gene Names: RAF1RAF
EC: 2.7.1 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for P04049 (Homo sapiens)
Explore P04049 
Go to UniProtKB:  P04049
NIH Common Fund Data Resources
PHAROS  P04049
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.17α = 90
b = 71.88β = 90
c = 100.2γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1999-07-22 
  • Released Date: 1999-08-02 
  • Deposition Author(s): Nassar, N.

Revision History 

  • Version 1.0: 1999-08-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance