PDBsum entry 1q1s

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Protein transport PDB id
Jmol PyMol
Protein chains
15 a.a.
434 a.a. *
Waters ×305
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Mouse importin alpha- phosphorylated sv40 cn peptide complex
Structure: Large t antigen. Chain: a, b. Fragment: cn peptide - ser112 chemically phosphorylated. Engineered: yes. Mutation: yes. Importin alpha-2 subunit. Chain: c. Fragment: nls binding domain (70-529). Synonym: karyopherin alpha-2 subunit, srp1-alpha, rag
Source: Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of this peptide is naturally found in simian virus 40 (sv40) large tumor-antigen. Ser112 was chemically phosphorylated. Mus musculus. House mouse. Organism_taxid: 10090. Gene: kpna2 or rch1.
2.30Å     R-factor:   0.198     R-free:   0.221
Authors: M.R.M.Fontes,T.Teh,G.Toth,A.John,I.Pavo,D.A.Jans,B.Kobe
Key ref: M.R.Fontes et al. (2003). Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha. Biochem J, 375, 339-349. PubMed id: 12852786
22-Jul-03     Release date:   30-Mar-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P03070  (LT_SV40) -  Large T antigen
708 a.a.
15 a.a.*
Protein chain
Pfam   ArchSchema ?
P52293  (IMA2_MOUSE) -  Importin subunit alpha-1
529 a.a.
434 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     protein import into nucleus   1 term 
  Biochemical function     protein transporter activity     1 term  


Biochem J 375:339-349 (2003)
PubMed id: 12852786  
Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-alpha.
M.R.Fontes, T.Teh, G.Toth, A.John, I.Pavo, D.A.Jans, B.Kobe.
The nuclear import of simian-virus-40 large T-antigen (tumour antigen) is enhanced via phosphorylation by the protein kinase CK2 at Ser112 in the vicinity of the NLS (nuclear localization sequence). To determine the structural basis of the effect of the sequences flanking the basic cluster KKKRK, and the effect of phosphorylation on the recognition of the NLS by the nuclear import factor importin-alpha (Impalpha), we co-crystallized non-autoinhibited Impalpha with peptides corresponding to the phosphorylated and non-phosphorylated forms of the NLS, and determined the crystal structures of the complexes. The structures show that the amino acids N-terminally flanking the basic cluster make specific contacts with the receptor that are distinct from the interactions between bipartite NLSs and Impalpha. We confirm the important role of flanking sequences using binding assays. Unexpectedly, the regions of the peptides containing the phosphorylation site do not make specific contacts with the receptor. Binding assays confirm that phosphorylation does not increase the affinity of the T-antigen NLS to Impalpha. We conclude that the sequences flanking the basic clusters in NLSs play a crucial role in nuclear import by modulating the recognition of the NLS by Impalpha, whereas phosphorylation of the T-antigen enhances nuclear import by a mechanism that does not involve a direct interaction of the phosphorylated residue with Impalpha.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21146412 N.E.Davey, G.Travé, and T.J.Gibson (2011).
How viruses hijack cell regulation.
  Trends Biochem Sci, 36, 159-169.  
20701745 J.B.Kelley, A.M.Talley, A.Spencer, D.Gioeli, and B.M.Paschal (2010).
Karyopherin alpha7 (KPNA7), a divergent member of the importin alpha family of nuclear import receptors.
  BMC Cell Biol, 11, 63.  
21182795 J.D.Nardozzi, K.Lott, and G.Cingolani (2010).
Phosphorylation meets nuclear import: a review.
  Cell Commun Signal, 8, 32.  
19514019 L.M.McLane, and A.H.Corbett (2009).
Nuclear localization signals and human disease.
  IUBMB Life, 61, 697-706.  
19520826 S.Kosugi, M.Hasebe, M.Tomita, and H.Yanagawa (2009).
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs.
  Proc Natl Acad Sci U S A, 106, 10171-10176.  
19001369 S.Kosugi, M.Hasebe, N.Matsumura, H.Takashima, E.Miyamoto-Sato, M.Tomita, and H.Yanagawa (2009).
Six Classes of Nuclear Localization Signals Specific to Different Binding Grooves of Importin {alpha}.
  J Biol Chem, 284, 478-485.  
18586821 L.M.McLane, K.F.Pulliam, S.E.Devine, and A.H.Corbett (2008).
The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus.
  Nucleic Acids Res, 36, 4317-4326.  
18054235 P.Tompa, and M.Fuxreiter (2008).
Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions.
  Trends Biochem Sci, 33, 2-8.  
18227062 S.A.Adam, K.Sengupta, and R.D.Goldman (2008).
Regulation of nuclear lamin polymerization by importin alpha.
  J Biol Chem, 283, 8462-8468.  
17170104 A.Lange, R.E.Mills, C.J.Lange, M.Stewart, S.E.Devine, and A.H.Corbett (2007).
Classical nuclear localization signals: definition, function, and interaction with importin alpha.
  J Biol Chem, 282, 5101-5105.  
17426132 N...Knudsen, F.C.Nielsen, L.Vinther, R.Bertelsen, S.Holten-Andersen, S.E.Liberti, R.Hofstra, K.Kooi, and L.J.Rasmussen (2007).
Nuclear localization of human DNA mismatch repair protein exonuclease 1 (hEXO1).
  Nucleic Acids Res, 35, 2609-2619.  
17163983 S.M.Stinnett, E.A.Espeso, L.Cobeño, L.Araújo-Bazán, and A.M.Calvo (2007).
Aspergillus nidulans VeA subcellular localization is dependent on the importin alpha carrier and on light.
  Mol Microbiol, 63, 242-255.  
17000757 B.Friedrich, C.Quensel, T.Sommer, E.Hartmann, and M.Köhler (2006).
Nuclear localization signal and protein context both mediate importin alpha specificity of nuclear import substrates.
  Mol Cell Biol, 26, 8697-8709.  
16809347 J.S.Hontz, M.T.Villar-Lecumberri, B.M.Potter, M.D.Yoder, L.A.Dreyfus, and J.H.Laity (2006).
Differences in crystal and solution structures of the cytolethal distending toxin B subunit: Relevance to nuclear translocation and functional activation.
  J Biol Chem, 281, 25365-25372.
PDB code: 2f1n
16439554 R.Kitamura, T.Sekimoto, S.Ito, S.Harada, H.Yamagata, H.Masai, Y.Yoneda, and K.Yanagi (2006).
Nuclear import of Epstein-Barr virus nuclear antigen 1 mediated by NPI-1 (Importin alpha5) is up- and down-regulated by phosphorylation of the nuclear localization signal for which Lys379 and Arg380 are essential.
  J Virol, 80, 1979-1991.  
16345111 S.Schlummer, R.Vetter, N.Kuder, A.Henkel, Y.X.Chen, Y.M.Li, J.Kuhlmann, and H.Waldmann (2006).
Influence of serine O-glycosylation or O-phosphorylation close to the vJun nuclear localisation sequence on nuclear import.
  Chembiochem, 7, 88-97.  
15605376 D.Lind, S.Franken, J.Kappler, J.Jankowski, and K.Schilling (2005).
Characterization of the neuronal marker NeuN as a multiply phosphorylated antigen with discrete subcellular localization.
  J Neurosci Res, 79, 295-302.  
16190981 G.Alvisi, D.A.Jans, J.Guo, L.A.Pinna, and A.Ripalti (2005).
A protein kinase CK2 site flanking the nuclear targeting signal enhances nuclear transport of human cytomegalovirus ppUL44.
  Traffic, 6, 1002-1013.  
15367661 H.N.Nuthall, K.Joachim, and S.Stifani (2004).
Phosphorylation of serine 239 of Groucho/TLE1 by protein kinase CK2 is important for inhibition of neuronal differentiation.
  Mol Cell Biol, 24, 8395-8407.  
14998990 M.T.Harreman, T.M.Kline, H.G.Milford, M.B.Harben, A.E.Hodel, and A.H.Corbett (2004).
Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals.
  J Biol Chem, 279, 20613-20621.  
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.