PDBsum entry 2dwg

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protein Protein-protein interface(s) links
Protein binding PDB id
Jmol PyMol
Protein chains
158 a.a. *
Waters ×31
* Residue conservation analysis
PDB id:
Name: Protein binding
Title: Run domain of rap2 interacting protein x, crystallized in p2(1)2(1)2(1) space group
Structure: Protein rufy3. Chain: a, b. Fragment: run domain. Synonym: rap2-interacting protein x, ripx. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: rufy3, d5bwg0860e, ripx. Expressed in: cell free synthesis. Other_details: cell free protein synthesis
Biol. unit: Dimer (from PQS)
3.22Å     R-factor:   0.210     R-free:   0.292
Authors: M.Kukimoto-Niino,K.Murayama,M.Shirouzu,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
M.Kukimoto-Niino et al. (2006). Crystal structure of the RUN domain of the RAP2-interacting protein x. J Biol Chem, 281, 31843-31853. PubMed id: 16928684 DOI: 10.1074/jbc.M604960200
11-Aug-06     Release date:   24-Oct-06    
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Protein chains
Pfam   ArchSchema ?
Q9D394  (RUFY3_MOUSE) -  Protein RUFY3
469 a.a.
158 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M604960200 J Biol Chem 281:31843-31853 (2006)
PubMed id: 16928684  
Crystal structure of the RUN domain of the RAP2-interacting protein x.
M.Kukimoto-Niino, T.Takagi, R.Akasaka, K.Murayama, T.Uchikubo-Kamo, T.Terada, M.Inoue, S.Watanabe, A.Tanaka, Y.Hayashizaki, T.Kigawa, M.Shirouzu, S.Yokoyama.
Rap2-interacting protein x (RPIPx) is a homolog of RPIP8, a specific effector of Rap2 GTPase. The N-terminal region of RPIP8, which contains the RUN domain, interacts with Rap2. Using cell-free synthesis and NMR, we determined that the region encompassing residues 83-255 of mouse RPIPx, which is 40-residues larger than the predicted RUN domain (residues 113-245), is the minimum fragment that forms a correctly folded protein. This fragment, the RPIPx RUN domain, interacted specifically with Rap2B in vitro in a nucleotide-dependent manner. The crystal structure of the RPIPx RUN domain was determined at 2.0 A of resolution by the multiwavelength anomalous dispersion (MAD) method. The RPIPx RUN domain comprises eight anti-parallel alpha-helices, which form an extensive hydrophobic core, followed by an extended segment. The residues in the core region are highly conserved, suggesting the conservation of the RUN domain-fold among the RUN domain-containing proteins. The residues forming a positively charged surface are conserved between RPIP8 and its homologs, suggesting that this surface is important for Rap2 binding. In the crystal the putative Rap2 binding site of the RPIPx RUN domain interacts with the extended segment in a segment-swapping manner.
  Selected figure(s)  
Figure 2.
FIGURE 2. ^1H (upper) and ^1H-^15N HSQC (lower) spectra of four RPIPx domains, corresponding to residues 83-245 (A), 83-255 (B), 83-265 (C), and 83-275 (D).
Figure 3.
FIGURE 3. Specific interaction of the RPIPx RUN domain with Rap2 in vitro. GST-Rap2B in the GTP S and GDPNP forms interacted with the His-tagged RPIPx RUN domain, whereas GST-Rap2B in the GDP form did not bind to the His-tagged RPIPx RUN domain. GST-Rap1A in the GDP, GTP S, and GDPNP forms and GST alone did not bind to the His-tagged RPIPx RUN domain.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 31843-31853) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20974968 Q.Sun, W.Westphal, K.N.Wong, I.Tan, and Q.Zhong (2010).
Rubicon controls endosome maturation as a Rab7 effector.
  Proc Natl Acad Sci U S A, 107, 19338-19343.  
20100911 S.Pankiv, E.A.Alemu, A.Brech, J.A.Bruun, T.Lamark, A.Overvatn, G.Bjørkøy, and T.Johansen (2010).
FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport.
  J Cell Biol, 188, 253-269.  
19400726 A.P.Barnes, and F.Polleux (2009).
Establishment of axon-dendrite polarity in developing neurons.
  Annu Rev Neurosci, 32, 347-381.  
19645719 E.Yaman, R.Gasper, C.Koerner, A.Wittinghofer, and U.H.Tazebay (2009).
RasGEF1A and RasGEF1B are guanine nucleotide exchange factors that discriminate between Rap GTP-binding proteins and mediate Rap2-specific nucleotide exchange.
  FEBS J, 276, 4607-4616.  
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
20514218 Y.Nie, C.Viola, C.Bieniossek, S.Trowitzsch, L.S.Vijay-Achandran, M.Chaillet, F.Garzoni, and I.Berger (2009).
Getting a grip on complexes.
  Curr Genomics, 10, 558-572.  
18210369 B.A.Manjasetty, A.P.Turnbull, S.Panjikar, K.Büssow, and M.R.Chance (2008).
Automated technologies and novel techniques to accelerate protein crystallography for structural genomics.
  Proteomics, 8, 612-625.  
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.