2GIL

Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution

• PDB DOI: https://doi.org/10.2210/pdb2GIL/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-03-29 Released: 2006-06-27 
• Deposition Author(s): Bergbrede, T., Pylypenko, O., Rak, A., Alexandrov, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.277 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Structure of the extremely slow GTPase Rab6A in the GTP bound form at 1.8 resolution

Bergbrede, T., Pylypenko, O., Rak, A., Alexandrov, A.

(2005) J Struct Biol 152: 235-238

• PubMed: 16332443 
• DOI: https://doi.org/10.1016/j.jsb.2005.10.001
• Primary Citation of Related Structures:  
  2GIL


• PubMed Abstract: 
  

  Rab/Ypt GTPases represent a>60 member large family of membrane traffic regulators in eukaryotic cells. Members of this group display intrinsic GTPase activity varying over two orders of magnitude. Here, we show that Rab6A represents the RabGTPase with the slowest spontaneous GTPase activity yet measured (5x10(-6)s(-1)). Due to the very low intrinsic hydrolysis rate we were able to crystallise and solve the structure of the Rab6A:GTP complex to 1.82A resolution. Analysis of the structure suggests that low catalytic activity of the Rab6A might be due to high flexibility of the Switch II region and a low degree of constraint of critically important for catalysis Gln 72.

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Organizational Affiliation: 

Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Str. 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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 76.67 kDa 
• Atom Count: 6,065 
• Modelled Residue Count: 645 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-6A	A, B, C, D	162	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20340 (Homo sapiens) Explore P20340  Go to UniProtKB:  P20340
PHAROS:  P20340 GTEx:  ENSG00000175582

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	E [auth A], G [auth B], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.277 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.008	α = 90
b = 124.853	β = 107.57
c = 66.162	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ProDC	data collection
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-27 
Deposition Author(s): Bergbrede, T., Pylypenko, O., Rak, A., Alexandrov, K.

Revision History  

• Version 1.0: 2006-06-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description