PDBsum entry 1xke

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Protein transport PDB id
Jmol PyMol
Protein chain
130 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Solution structure of the second ran-binding domain from human ranbp2
Structure: Ran-binding protein 2. Chain: a. Fragment: ran-binding domain 2 (ranbd2). Synonym: ranbp2, nuclear pore complex protein nup358, nucleoporin nup358, 358 kda nucleoporin, p270. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: J.P.Geyer,R.Doeker,W.Kremer,X.Zhao,J.Kuhlmann,H.R.Kalbitzer
Key ref:
J.P.Geyer et al. (2005). Solution structure of the Ran-binding domain 2 of RanBP2 and its interaction with the C terminus of Ran. J Mol Biol, 348, 711-725. PubMed id: 15826666 DOI: 10.1016/j.jmb.2005.02.033
28-Sep-04     Release date:   19-Apr-05    
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Protein chain
Pfam   ArchSchema ?
P49792  (RBP2_HUMAN) -  E3 SUMO-protein ligase RanBP2
3224 a.a.
130 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     intracellular transport   1 term 


DOI no: 10.1016/j.jmb.2005.02.033 J Mol Biol 348:711-725 (2005)
PubMed id: 15826666  
Solution structure of the Ran-binding domain 2 of RanBP2 and its interaction with the C terminus of Ran.
J.P.Geyer, R.Döker, W.Kremer, X.Zhao, J.Kuhlmann, H.R.Kalbitzer.
The termination of export processes from the nucleus to the cytoplasm in higher eukaryotes is mediated by binding of the small GTPase Ran as part of the export complexes to the Ran-binding domains (RanBD) of Ran-binding protein 2 (RanBP2) of the nuclear pore complex. So far, the structures of the first RanBD of RanBP2 and of RanBP1 in complexes with Ran have been known from X-ray crystallographic studies. Here we report the NMR solution structure of the uncomplexed second RanBD of RanBP2. The structure shows a pleckstrin homology (PH) fold featuring two almost orthogonal beta-sheets consisting of three and four strands and an alpha-helix sitting on top. This is in contrast to the RanBD in the crystal structure complexes in which one beta-strand is missing. That is probably due to the binding of the C-terminal alpha-helix of Ran to the RanBD in these complexes. To analyze the interaction between RanBD2 and the C terminus of Ran, NMR-titration studies with peptides comprising the six or 28 C-terminal residues of Ran were performed. While the six-residue peptide alone does not bind to RanBD2 in a specific manner, the 28-residue peptide, including the entire C-terminal helix of Ran, binds to RanBD2 in a manner analogous to the crystal structures. By solving the solution structure of the 28mer peptide alone, we confirmed that it adopts a stable alpha-helical structure like in native Ran and therefore serves as a valid model of the Ran C terminus. These results support current models that assume recognition of the transport complexes by the RanBDs through the Ran C terminus that is exposed in these complexes.
  Selected figure(s)  
Figure 4.
Figure 4. Surface charge distribution of RanBD2 and interaction with peptides. (a) Surface charge distribution in RanBD2. The molecule is shown in the same orientation as in Figure 3(a). (b) Same as (a) after a z-rotation of 90°. The basic patch supposed to bind the DEDDDL motif can be seen in the center. (c) Putative interaction sites of the DEDDDL-peptide mapped on the RanBD2 surface. The molecule is shown in the same orientation as in (a). Residues showing a chemical shift change larger than the mean value plus one half standard deviation, one standard deviation and two standard deviations for a twofold molar excess of the peptide are colored yellow, orange and red, respectively. (d) Same as (c) after a z-rotation of 90°.
Figure 5.
Figure 5. Solution structure of Ran.189-216 (a) Ribbon representation of the lowest-energy structure. (b) Backbone representation of the 20 lowest-energy structures from the calculation.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 711-725) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21364925 K.Langer, C.Dian, V.Rybin, C.W.Müller, and C.Petosa (2011).
Insights into the Function of the CRM1 Cofactor RanBP3 from the Structure of Its Ran-Binding Domain.
  PLoS One, 6, e17011.
PDB codes: 2y8f 2y8g
18650440 H.Li, S.Koshiba, F.Hayashi, N.Tochio, T.Tomizawa, T.Kasai, T.Yabuki, Y.Motoda, T.Harada, S.Watanabe, M.Inoue, Y.Hayashizaki, A.Tanaka, T.Kigawa, and S.Yokoyama (2008).
Structure of the C-terminal phosphotyrosine interaction domain of Fe65L1 complexed with the cytoplasmic tail of amyloid precursor protein reveals a novel peptide binding mode.
  J Biol Chem, 283, 27165-27178.
PDB codes: 1wgu 2roz 2ysz 2yt0 2yt1
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 codes are shown on the right.