4AII | pdb_00004aii

Crystal structure of the rat REM2 GTPase - G domain bound to GDP

• PDB DOI: https://doi.org/10.2210/pdb4AII/pdb

• Classification: GTP-BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-02-10 Released: 2012-06-13 
• Deposition Author(s): Reymond, P., Coquard, A., Chenon, M., Zeghouf, M., El Marjou, A., Thompson, A., Menetrey, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.324 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Structure of the Gdp-Bound G Domain of the Rgk Protein Rem2.

Reymond, P., Coquard, A., Chenon, M., Zeghouf, M., El Marjou, A., Thompson, A., Menetrey, J.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 626

• PubMed: 22684057 
• DOI: https://doi.org/10.1107/S1744309112013541
• Primary Citation of Related Structures:  
  4AII


• PubMed Abstract: 
  

  RGK proteins are atypical small GTP-binding proteins that are involved in the regulation of voltage-dependent calcium channels and actin cytoskeleton remodelling. The structure of the Rem2 G domain bound to GDP is reported here in a monoclinic crystal form at 2.66 Å resolution. It is very similar to the structure determined previously from an orthorhombic crystal form. However, differences in the crystal-packing environment revealed that the switch I and switch II regions are flexible and not ordered as previously reported. Comparison of the available RGK protein structures along with those of other small GTP-binding proteins highlights two structural features characteristic of this atypical family and suggests that the conserved tryptophan residue in the DXWEX motif may be a structural determinant of the nucleotide-binding affinity.

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Organizational Affiliation: 

Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 91198 Gif-sur-Yvette, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.24 kDa 
• Atom Count: 2,258 
• Modelled Residue Count: 290 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-BINDING PROTEIN REM 2	A, B	180	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q9WTY2 (Rattus norvegicus) Explore Q9WTY2  Go to UniProtKB:  Q9WTY2

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.324 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.916	α = 90
b = 59.374	β = 101.51
c = 57.297	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Reymond, P., Coquard, A., Chenon, M., Zeghouf, M., El Marjou, A., Thompson, A., Menetrey, J.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2012-06-20
  Changes: Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description