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PDBsum entry 2iey

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protein ligands Protein-protein interface(s) links
Signaling protein PDB id
2iey
Jmol
Contents
Protein chains
164 a.a. *
163 a.a. *
Ligands
GDP ×2
Waters ×11
* Residue conservation analysis
PDB id:
2iey
Name: Signaling protein
Title: Crystal structure of mouse rab27b bound to gdp in hexagonal group
Structure: Ras-related protein rab-27b. Chain: a, b. Fragment: soluble domain. Engineered: yes. Mutation: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
3.18Å     R-factor:   0.292     R-free:   0.345
Authors: L.M.G.Chavas,S.Torii,H.Kamikubo,M.Kawasaki,K.Ihara,R.Kato,M. T.Izumi,S.Wakatsuki
Key ref:
L.M.Chavas et al. (2007). Structure of the small GTPase Rab27b shows an unexpected swapped dimer. Acta Crystallogr D Biol Crystallogr, 63, 769-779. PubMed id: 17582168 DOI: 10.1107/S0907444907019725
Date:
19-Sep-06     Release date:   01-May-07    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q99P58  (RB27B_MOUSE) -  Ras-related protein Rab-27B
Seq:
Struc:
218 a.a.
164 a.a.
Protein chain
Pfam   ArchSchema ?
Q99P58  (RB27B_MOUSE) -  Ras-related protein Rab-27B
Seq:
Struc:
218 a.a.
163 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     signal transduction   6 terms 
  Biochemical function     GTP binding     2 terms  

 

 
DOI no: 10.1107/S0907444907019725 Acta Crystallogr D Biol Crystallogr 63:769-779 (2007)
PubMed id: 17582168  
 
 
Structure of the small GTPase Rab27b shows an unexpected swapped dimer.
L.M.Chavas, S.Torii, H.Kamikubo, M.Kawasaki, K.Ihara, R.Kato, M.Kataoka, T.Izumi, S.Wakatsuki.
 
  ABSTRACT  
 
Members of the Rab family of small GTPases regulate membrane traffic within the cell by recruiting their specific effectors in a nucleotide-dependent manner. The Rab27 subfamily consists of Rab27a and Rab27b, which share 70% sequence identity. By interacting with a large set of effector proteins such as melanophilin and granuphilin, both Rab27a and Rab27b regulate the exocytosis of secretory lysosomes. Here, the crystal structures of mouse Rab27b in complex with GDP have been determined in three distinct crystal lattices. Surprisingly, Rab27b-GDP exists in an open conformation with protruding switch and interswitch regions, which are stabilized through dimerization by means of domain-swapping in the crystals. In contrast, small-angle X-ray scattering measurements showed an extended monomer form of Rab27b in solution. The observed dimer formation of Rab27b-GDP in the crystals would restrain the highly flexible switch regions. Possible biological implications of this atypical structure of Rab27b and its plausible influence in effector interaction are discussed.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Arrangement of Rab27b secondary-structural elements as a topology diagram. Arrows and ovals represent -strands and -helices, respectively. The two molecules in the dimer are coloured differently. Individual elements are labelled and the N- and C-termini are indicated.
Figure 5.
Figure 5 -Sheet of switch/interswitch regions. Interaction diagram representing the hydrogen-bonding interactions between monomers in the P6[5]22 (a) and C2 (b) lattices. Residues are labelled. Strands are coloured according to the molecule that they belong to. Hydrogen bonds are indicated by arrows from the donor residue to the acceptor residue. A pseudo-twofold axis is marked in the C2 arrangement between the two Thr41 residues. The diagram for the P2[1]2[1]2[1] lattice is identical to that for the C2 lattice.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2007, 63, 769-779) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19489729 A.Edwards (2009).
Large-scale structural biology of the human proteome.
  Annu Rev Biochem, 78, 541-568.  
19427324 A.F.Neuwald (2009).
The charge-dipole pocket: a defining feature of signaling pathway GTPase on/off switches.
  J Mol Biol, 390, 142-153.  
19141279 R.Recacha, A.Boulet, F.Jollivet, S.Monier, A.Houdusse, B.Goud, and A.R.Khan (2009).
Structural basis for recruitment of Rab6-interacting protein 1 to Golgi via a RUN domain.
  Structure, 17, 21-30.
PDB code: 3cwz
18650931 K.Gotthardt, M.Weyand, A.Kortholt, P.J.Van Haastert, and A.Wittinghofer (2008).
Structure of the Roc-COR domain tandem of C. tepidum, a prokaryotic homologue of the human LRRK2 Parkinson kinase.
  EMBO J, 27, 2239-2249.
PDB codes: 3dpt 3dpu
  18607085 L.M.Chavas, K.Ihara, M.Kawasaki, R.Kato, T.Izumi, and S.Wakatsuki (2008).
Purification, crystallization and preliminary X-ray crystallographic analysis of Rab27a GTPase in complex with exophilin4/Slp2-a effector.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 599-601.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.