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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.00 kDa 
• Atom Count: 1579 
• Modelled Residue Count: 176 
• Deposited Residue Count: 176 
• Unique protein chains: 1

4RKE

Drosophila melanogaster Rab2 bound to GMPPNP

• PDB DOI: 10.2210/pdb4RKE/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-10-13 Released: 2014-12-10 
• Deposition Author(s): Lardong, J.A., Driller, J.H., Depner, H., Weise, C., Petzoldt, A., Wahl, M.C., Sigrist, S.J., Loll, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Literature

Structures of Drosophila melanogaster Rab2 and Rab3 bound to GMPPNP.

Lardong, J.A., Driller, J.H., Depner, H., Weise, C., Petzoldt, A., Wahl, M.C., Sigrist, S.J., Loll, B.

(2015) Acta Crystallogr Sect F Struct Biol Cryst Commun 71: 34-40

• PubMed: 25615965 
• DOI: 10.1107/S2053230X1402617X
• Primary Citation of Related Structures:  
  4RKE, 4RKF


• PubMed Abstract: 
  

Rab GTPases belong to the large family of Ras proteins. They act as key regulators of membrane organization and intracellular trafficking. Functionally, they act as switches. In the active GTP-bound form they can bind to effector proteins to facilitate the delivery of transport vesicles. Upon stimulation, the GTP is hydrolyzed and the Rab proteins undergo conformational changes in their switch regions. This study focuses on Rab2 and Rab3 from Drosophila melanogaster. Whereas Rab2 is involved in vesicle transport between the Golgi and the endoplasmatic reticulum, Rab3 is a key player in exocytosis, and in the synapse it is involved in the assembly of the presynaptic active zone. Here, high-resolution crystal structures of Rab2 and Rab3 in complex with GMPPNP and Mg2+ are presented. In the structure of Rab3 a modified cysteine residue is observed with an enigmatic electron density attached to its thiol function.

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Organizational Affiliation: 

Institut für Chemie und Biochemie Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 15195 Berlin, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH01619p	A	176	Drosophila melanogaster	Mutation(s): 1  Gene Names: rab2, CG3269, Dmel_CG3269, Rab2, Dmel\CG3269, DmRab2, DRAB2, DRab2, Drab2, O18333
UniProt
Find proteins for O18333 (Drosophila melanogaster) Explore O18333  Go to UniProtKB:  O18333

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
1PE	D [auth A], E [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.355	α = 90
b = 81.355	β = 90
c = 53.128	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-13 
• Released Date: 2014-12-10 
Deposition Author(s): Lardong, J.A., Driller, J.H., Depner, H., Weise, C., Petzoldt, A., Wahl, M.C., Sigrist, S.J., Loll, B.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2015-01-07
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Database references