PDBsum entry 2q5d

Go to PDB code: 
protein Protein-protein interface(s) links
Protein transport PDB id
Protein chains
871 a.a. *
36 a.a. *
23 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Crystal structure of human importin beta bound to the snurpo domain second crystal form
Structure: Importin beta-1 subunit. Chain: a, b. Synonym: karyopherin beta-1 subunit, nuclear factor p97, im engineered: yes. Snurportin-1. Chain: c, d. Fragment: n-terminal domain (25-64). Synonym: RNA u transporter 1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: kpnb1, ntf97. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606
3.20Å     R-factor:   0.303     R-free:   0.328
Authors: G.Mitrousis,G.Cingolani
Key ref:
G.Mitrousis et al. (2008). Molecular basis for the recognition of snurportin 1 by importin beta. J Biol Chem, 283, 7877-7884. PubMed id: 18187419 DOI: 10.1074/jbc.M709093200
31-May-07     Release date:   22-Jan-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q14974  (IMB1_HUMAN) -  Importin subunit beta-1
876 a.a.
871 a.a.
Protein chain
Pfam   ArchSchema ?
O95149  (SPN1_HUMAN) -  Snurportin-1
360 a.a.
36 a.a.
Protein chain
Pfam   ArchSchema ?
O95149  (SPN1_HUMAN) -  Snurportin-1
360 a.a.
23 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     endoplasmic reticulum tubular network   11 terms 
  Biological process     viral reproduction   16 terms 
  Biochemical function     protein binding     8 terms  


DOI no: 10.1074/jbc.M709093200 J Biol Chem 283:7877-7884 (2008)
PubMed id: 18187419  
Molecular basis for the recognition of snurportin 1 by importin beta.
G.Mitrousis, A.S.Olia, N.Walker-Kopp, G.Cingolani.
The nuclear import of uridine-rich ribonucleoproteins is mediated by the transport adaptor snurportin 1 (SNP1). Similar to importin alpha, SNP1 uses an N-terminal importin beta binding (sIBB) domain to recruit the receptor importin beta and gain access to the nucleus. In this study, we demonstrate that the sIBB domain has a bipartite nature, which contains two distinct binding determinants for importin beta. The first determinant spans residues 25-65 and includes the previously identified importin alpha IBB (alphaIBB) region of homology. The second binding determinant encompasses residues 1-24 and resembles region 1011-1035 of the nucleoporin 153 (Nup153). The two binding determinants synergize within the sIBB domain to confer a low nanomolar binding affinity for importin beta (K(d) approximately 2 nm) in an interaction that, in vitro, is displaced by RanGTP. We propose that in vivo the synergy of Nup153 and nuclear RanGTP promotes translocation of uridine-rich ribonucleoproteins into the nucleus.
  Selected figure(s)  
Figure 2.
FIGURE 2. Structural plasticity of importin β bound to the sIBB-(25-65) domain. a, ribbon diagram of the asymmetric unit content of crystal form II, determined at 3.2 Å resolution. The two complexes in the asymmetric unit have different conformations. In complex B, on the left (in cyan), importin β adopts an open conformation, and only the sIBB-(40-65) helix is visible (in yellow). In complex A, on the right (in green), importin β has a conformation identical to crystal form I, and all residues for the sIBB-(25-65) domain are visible (in magenta). b, superimposition of the importin β structures from complex A (closed) and B (open) reveals deviations up to 20 Å in the C terminus of the protein.
Figure 3.
FIGURE 3. sIBB-(25-65) domain versus IBB-(11-54) domain. a, left panel, structure of importin β- IBB complex (in purple and blue, respectively) superimposed to that of the importin β-sIBB-(25-65) complex (in green and magenta, respectively) of crystal form I. Right panel, blowup of the IBB and sIBB-(25-65) domains (colored in blue and magenta, respectively) translated out of the superimposition. Significant differences are observed in the structure of the two peptides. b, schematic diagram of the interactions between HEAT repeats 7-19 of importin β and the sIBB-(25-65) domain (top) as compared with the IBB-(11-54) domain (bottom). HEAT repeats are referred to as H7-19. Colored in red in the primary sequence of the sIBB-(25-65) and IBB-(11-54) domain are identical residues. Intermolecular polar and hydrophobic interactions are shown as red and green lines, respectively. Intramolecular contacts within IBB domains are indicated by red brackets.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 7877-7884) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21139563 M.Grünwald, and F.Bono (2011).
Structure of Importin13-Ubc9 complex: nuclear import and release of a key regulator of sumoylation.
  EMBO J, 30, 427-438.
PDB code: 2xwu
20811366 A.R.Lowe, J.J.Siegel, P.Kalab, M.Siu, K.Weis, and J.T.Liphardt (2010).
Selectivity mechanism of the nuclear pore complex characterized by single cargo tracking.
  Nature, 467, 600-603.  
20421206 E.Kühn-Hölsken, C.Lenz, A.Dickmanns, H.H.Hsiao, F.M.Richter, B.Kastner, R.Ficner, and H.Urlaub (2010).
Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry.
  Nucleic Acids Res, 38, 5581-5593.  
20826343 J.K.Forwood, A.Lange, U.Zachariae, M.Marfori, C.Preast, H.Grubmüller, M.Stewart, A.H.Corbett, and B.Kobe (2010).
Quantitative structural analysis of importin-β flexibility: paradigm for solenoid protein structures.
  Structure, 18, 1171-1183.
PDB code: 3nd2
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
19421156 E.W.Debler, G.Blobel, and A.Hoelz (2009).
Nuclear transport comes full circle.
  Nat Struct Mol Biol, 16, 457-459.  
19488829 K.E.Lundin, O.E.Simonson, P.M.Moreno, E.M.Zaghloul, I.I.Oprea, M.G.Svahn, and C.I.Smith (2009).
Nanotechnology approaches for gene transfer.
  Genetica, 137, 47-56.  
20514217 N.Freitas, and C.Cunha (2009).
Mechanisms and signals for the nuclear import of proteins.
  Curr Genomics, 10, 550-557.  
19208638 P.M.Moreno, M.Wenska, K.E.Lundin, O.Wrange, R.Strömberg, and C.I.Smith (2009).
A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids.
  Nucleic Acids Res, 37, 1925-1935.  
19389996 T.Monecke, T.Güttler, P.Neumann, A.Dickmanns, D.Görlich, and R.Ficner (2009).
Crystal structure of the nuclear export receptor CRM1 in complex with Snurportin1 and RanGTP.
  Science, 324, 1087-1091.
PDB code: 3gjx
19339969 X.Dong, A.Biswas, K.E.Süel, L.K.Jackson, R.Martinez, H.Gu, and Y.M.Chook (2009).
Structural basis for leucine-rich nuclear export signal recognition by CRM1.
  Nature, 458, 1136-1141.
PDB code: 3gb8
19339972 X.Dong, A.Biswas, and Y.M.Chook (2009).
Structural basis for assembly and disassembly of the CRM1 nuclear export complex.
  Nat Struct Mol Biol, 16, 558-560.  
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.