Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.44 kDa 
• Atom Count: 1429 
• Modelled Residue Count: 167 
• Deposited Residue Count: 167 
• Unique protein chains: 1

1KAO

CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAP2A WITH GDP

• PDB DOI: 10.2210/pdb1KAO/pdb

• Classification: GTP-BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-08-01 Released: 1997-12-24 
• Deposition Author(s): Cherfils, J., Menetrey, J., Le Bras, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Literature

Crystal structures of the small G protein Rap2A in complex with its substrate GTP, with GDP and with GTPgammaS.

Cherfils, J., Menetrey, J., Le Bras, G., Janoueix-Lerosey, I., de Gunzburg, J., Garel, J.R., Auzat, I.

(1997) EMBO J 16: 5582-5591

• PubMed: 9312017 
• DOI: 10.1093/emboj/16.18.5582
• Primary Citation of Related Structures:  
  1KAO, 2RAP


• PubMed Abstract: 
  

The small G protein Rap2A has been crystallized in complex with GDP, GTP and GTPgammaS. The Rap2A-GTP complex is the first structure of a small G protein with its natural ligand GTP. It shows that the hydroxyl group of Tyr32 forms a hydrogen bond with the gamma-phosphate of GTP and with Gly13. This interaction does not exist in the Rap2A-GTPgammaS complex. Tyr32 is conserved in many small G proteins, which probably also form this hydrogen bond with GTP. In addition, Tyr32 is structurally equivalent to a conserved arginine that binds GTP in trimeric G proteins. The actual participation of Tyr32 in GTP hydrolysis is not yet clear, but several possible roles are discussed. The conformational changes between the GDP and GTP complexes are located essentially in the switch I and II regions as described for the related oncoprotein H-Ras. However, the mobile segments vary in length and in the amplitude of movement. This suggests that even though similar regions might be involved in the GDP-GTP cycle of small G proteins, the details of the changes will be different for each G protein and will ensure the specificity of its interaction with a given set of cellular proteins.

---

Organizational Affiliation: 

Laboratoire d'Enzymologie et de Biochimie Structurales, UPR 9063-CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAP2A	A	167	Homo sapiens	Mutation(s): 0  Gene Names: RAP2A EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P10114 (Homo sapiens) Explore P10114  Go to UniProtKB:  P10114
PHAROS:  P10114 GTEx:  ENSG00000125249

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.826	α = 90
b = 35.315	β = 106.67
c = 58.356	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-08-01 
• Released Date: 1997-12-24 
Deposition Author(s): Cherfils, J., Menetrey, J., Le Bras, G.

Revision History  

• Version 1.0: 1997-12-24
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance