PDBsum entry 2eqb

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Endocytosis/exocytosis PDB id
Protein chains
171 a.a. *
93 a.a. *
PO4 ×2
Waters ×114
* Residue conservation analysis
PDB id:
Name: Endocytosis/exocytosis
Title: Crystal structure of the rab gtpase sec4p, the sec2p gef domain, and phosphate complex
Structure: Ras-related protein sec4. Chain: a. Fragment: residues 19-187. Synonym: suppressor of rho3 protein 6, rab gtpase sec4p. Engineered: yes. Rab guanine nucleotide exchange factor sec2. Chain: b, c. Fragment: gef domain, residues 51-142. Synonym: gdp-gtp exchange factor sec2.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.70Å     R-factor:   0.273     R-free:   0.298
Authors: Y.Sato,S.Fukai,R.Ishitani,O.Nureki
Key ref:
Y.Sato et al. (2007). Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state. Proc Natl Acad Sci U S A, 104, 8305-8310. PubMed id: 17488829 DOI: 10.1073/pnas.0701550104
30-Mar-07     Release date:   22-May-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P07560  (SEC4_YEAST) -  Ras-related protein SEC4
215 a.a.
171 a.a.*
Protein chains
Pfam   ArchSchema ?
P17065  (SEC2_YEAST) -  Rab guanine nucleotide exchange factor SEC2
759 a.a.
93 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein transport   2 terms 
  Biochemical function     GTP binding     1 term  


DOI no: 10.1073/pnas.0701550104 Proc Natl Acad Sci U S A 104:8305-8310 (2007)
PubMed id: 17488829  
Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state.
Y.Sato, S.Fukai, R.Ishitani, O.Nureki.
Vesicular transport during exocytosis is regulated by Rab GTPase (Sec4p in yeast), which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. Here, we report the crystal structure of the Sec2p GEF domain in a complex with the nucleotide-free Sec4p at 2.7 A resolution. Upon complex formation, the Sec2p helices approach each other, flipping the side chain of Phe-109 toward Leu-104 and Leu-108 of Sec2p. These three residues provide a hydrophobic platform to attract the side chains of Phe-49, Ile-53, and Ile-55 in the switch I region as well as Phe-57 and Trp-74 in the interswitch region of Sec4p. Consequently, the switch I and II regions are largely deformed, to create a flat hydrophobic interface that snugly fits the surface of the Sec2p coiled coil. These drastic conformational changes disrupt the interactions between switch I and the bound guanine nucleotide, which facilitates the GDP release. Unlike the recently reported 3.3 A structure of the Sec4p.Sec2p complex, our structure contains a phosphate ion bound to the P-loop, which may represent an intermediate state of the nucleotide exchange reaction.
  Selected figure(s)  
Figure 2.
Fig. 2. Sec4p·Sec2p binding interface. (a) Stereoview of the detailed Sec4p·Sec2p binding interface. The coloring scheme is the same as in Fig. 1b. Hydrogen bonds are shown by dotted orange lines. (b) Schematic representation of the Sec4p·Sec2p interface. The hydrogen bonds (with a 3.4 Å cutoff) are displayed as solid orange lines. The hydrophobic contacts (with a 4.0 Å cutoff) are displayed as dotted green lines. The labels of the switch I, interswitch, switch II, and other regions of Sec4p are highlighted in cyan, brown, pink, and gray, respectively. The labels of the sharply and moderately bent helices of Sec2p are highlighted in yellow and green, respectively.
Figure 4.
Fig. 4. Comparison of the Sec4p·GDP and Sec2p-bound Sec4p structures. (a) Comparison of the overall structures of Sec4p·GDP and Sec2p-bound Sec4p. Sec4p·GDP was superposed onto Sec4p in the Sec4p·Sec2p·phosphate complex, except for the residues 42–47, and the switch I (residues 48–56) and switch II (residues 76–93) regions. Sec4p·GDP is colored yellow, and Sec4p in the Sec4p·Sec2p·phosphate complex is colored as in Fig. 1b. The carbon atoms of the Sec4p-bound GDP are green, and the bound cobalt ion is yellow. (b) Comparison of the Sec2p binding region in the Sec4p·GDP and Sec2p-bound Sec4p structures. Coloring schemes are the same as in a. Dotted black arrows indicate positional changes of the amino acid residues.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20028791 B.A.McCray, E.Skordalakes, and J.P.Taylor (2010).
Disease mutations in Rab7 result in unregulated nucleotide exchange and inappropriate activation.
  Hum Mol Genet, 19, 1033-1047.
PDB code: 3law
20937701 S.Yoshimura, A.Gerondopoulos, A.Linford, D.J.Rigden, and F.A.Barr (2010).
Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors.
  J Cell Biol, 191, 367-381.  
19889643 Y.Fujioka, N.N.Noda, H.Nakatogawa, Y.Ohsumi, and F.Inagaki (2010).
Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy.
  J Biol Chem, 285, 1508-1515.
PDB codes: 3a7o 3a7p
20512138 Y.W.Wu, L.K.Oesterlin, K.T.Tan, H.Waldmann, K.Alexandrov, and R.S.Goody (2010).
Membrane targeting mechanism of Rab GTPases elucidated by semisynthetic protein probes.
  Nat Chem Biol, 6, 534-540.  
20176951 Y.Zhu, L.Hu, Y.Zhou, Q.Yao, L.Liu, and F.Shao (2010).
Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA.
  Proc Natl Acad Sci U S A, 107, 4699-4704.
PDB codes: 3l0i 3l0m
19522756 M.T.Lee, A.Mishra, and D.G.Lambright (2009).
Structural mechanisms for regulation of membrane traffic by rab GTPases.
  Traffic, 10, 1377-1389.  
20064470 S.Schoebel, L.K.Oesterlin, W.Blankenfeldt, R.S.Goody, and A.Itzen (2009).
RabGDI displacement by DrrA from Legionella is a consequence of its guanine nucleotide exchange activity.
  Mol Cell, 36, 1060-1072.
PDB codes: 3jz9 3jza
19414022 Y.An, C.Y.Chen, B.Moyer, P.Rotkiewicz, M.A.Elsliger, A.Godzik, I.A.Wilson, and W.E.Balch (2009).
Structural and functional analysis of the globular head domain of p115 provides insight into membrane tethering.
  J Mol Biol, 391, 26-41.
PDB codes: 3gq2 3grl
18559336 A.C.Figueiredo, C.Wasmeier, A.K.Tarafder, J.S.Ramalho, R.A.Baron, and M.C.Seabra (2008).
Rab3GEP is the non-redundant guanine nucleotide exchange factor for Rab27a in melanocytes.
  J Biol Chem, 283, 23209-23216.  
18369190 M.S.Yousef, H.Kamikubo, M.Kataoka, R.Kato, and S.Wakatsuki (2008).
Miranda cargo-binding domain forms an elongated coiled-coil homodimer in solution: implications for asymmetric cell division in Drosophila.
  Protein Sci, 17, 908-917.  
19026641 S.H.Lee, K.Baek, and R.Dominguez (2008).
Large nucleotide-dependent conformational change in Rab28.
  FEBS Lett, 582, 4107-4111.
PDB code: 3e5h
18585354 Y.Cai, H.F.Chin, D.Lazarova, S.Menon, C.Fu, H.Cai, A.Sclafani, D.W.Rodgers, E.M.De La Cruz, S.Ferro-Novick, and K.M.Reinisch (2008).
The structural basis for activation of the Rab Ypt1p by the TRAPP membrane-tethering complexes.
  Cell, 133, 1202-1213.
PDB code: 3cue
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.