1RYF

Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase

• PDB DOI: https://doi.org/10.2210/pdb1RYF/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-12-22 Released: 2004-01-27 
• Deposition Author(s): Ahmadian, M.R., Fiegen, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.223 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase

Fiegen, D., Haeusler, L.C., Blumenstein, L., Herbrand, U., Dvorsky, R., Vetter, I.R., Ahmadian, M.R.

(2004) J Biol Chem 279: 4743-4749

• PubMed: 14625275 
• DOI: https://doi.org/10.1074/jbc.M310281200
• Primary Citation of Related Structures:  
  1RYF, 1RYH


• PubMed Abstract: 
  

  Rac1b was recently identified in malignant colorectal tumors as an alternative splice variant of Rac1 containing a 19-amino acid insertion next to the switch II region. The structures of Rac1b in the GDP- and the GppNHp-bound forms, determined at a resolution of 1.75 A, reveal that the insertion induces an open switch I conformation and a highly mobile switch II. As a consequence, Rac1b has an accelerated GEF-independent GDP/GTP exchange and an impaired GTP hydrolysis, which is restored partially by GTPase-activating proteins. Interestingly, Rac1b is able to bind the GTPase-binding domain of PAK but not full-length PAK in a GTP-dependent manner, suggesting that the insertion does not completely abolish effector interaction. The presented study provides insights into the structural and biochemical mechanism of a self-activating GTPase.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.67 kDa 
• Atom Count: 2,917 
• Modelled Residue Count: 337 
• Deposited Residue Count: 406 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ras-related C3 botulinum toxin substrate 1 isoform Rac1b	A, B	203	Homo sapiens	Mutation(s): 0  EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
GTEx:  ENSG00000136238

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	D [auth A], F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GDP	PDBBind:  1RYF	Kd: 1.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.223 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.64	α = 90
b = 78.69	β = 90
c = 96.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-27 
Deposition Author(s): Ahmadian, M.R., Fiegen, D.

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description