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PDBsum entry 2c1t
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protein Protein-protein interface(s) links
Protein transport/membrane protein PDB id
2c1t

 

 

 

 

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Contents
Protein chains
423 a.a. *
36 a.a. *
39 a.a. *
Waters ×151
* Residue conservation analysis
PDB id:
2c1t
Name: Protein transport/membrane protein
Title: Structure of the kap60p:nup2 complex
Structure: Importin alpha subunit. Chain: a, b. Fragment: arm domain, residues 88-541. Synonym: kap60p, karyopherin alpha subunit, serine-rich RNA polymerase i suppressor protein. Engineered: yes. Mutation: yes. Nucleoporin nup2. Chain: c, d.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.60Å     R-factor:   0.205     R-free:   0.251
Authors: Y.Matsuura,M.Stewart
Key ref:
Y.Matsuura and M.Stewart (2005). Nup50/Npap60 function in nuclear protein import complex disassembly and importin recycling. EMBO J, 24, 3681-3689. PubMed id: 16222336 DOI: 10.1038/sj.emboj.7600843
Date:
20-Sep-05     Release date:   22-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q02821  (IMA1_YEAST) -  Importin subunit alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		542 a.a.
423 a.a.*
Protein chain
Pfam   ArchSchema ?
P32499  (NUP2_YEAST) -  Nucleoporin NUP2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		720 a.a.
36 a.a.
Protein chain
Pfam   ArchSchema ?
P32499  (NUP2_YEAST) -  Nucleoporin NUP2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		720 a.a.
39 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1038/sj.emboj.7600843 EMBO J 24:3681-3689 (2005)
PubMed id: 16222336  
 
 
Nup50/Npap60 function in nuclear protein import complex disassembly and importin recycling.
Y.Matsuura, M.Stewart.
 
  ABSTRACT  
 
Nuclear import of proteins containing classical nuclear localization signals (NLS) is mediated by the importin-alpha:beta complex that binds cargo in the cytoplasm and facilitates its passage through nuclear pores, after which nuclear RanGTP dissociates the import complex and the importins are recycled. In vertebrates, import is stimulated by nucleoporin Nup50, which has been proposed to accompany the import complex through nuclear pores. However, we show here that the Nup50 N-terminal domain actively displaces NLSs from importin-alpha, which would be more consistent with Nup50 functioning to coordinate import complex disassembly and importin recycling. The crystal structure of the importin-alpha:Nup50 complex shows that Nup50 binds at two sites on importin-alpha. One site overlaps the secondary NLS-binding site, whereas the second extends along the importin-alpha C-terminus. Mutagenesis indicates that interaction at both sites is required for Nup50 to displace NLSs. The Cse1p:Kap60p:RanGTP complex structure suggests how Nup50 is then displaced on formation of the importin-alpha export complex. These results provide a rationale for understanding the series of interactions that orchestrate the terminal steps of nuclear protein import.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Crystal structure of the Nup50:importin- complex and competition assays using structure-based mutants showed that Nup50 binds at two sites on importin- , and the NLS displacement by Nup50 requires interaction with both sites on importin- . (A) Overview of the Nup50:importin- complex with the 2F[o]-F[c] map around Nup50 contoured at 1 superimposed. Nup50 residues are shown in ball-and-stick format. (B) Electrostatic potential on importin- , with Nup50 removed, shaded from -9 kT/e (red) to +9 kT/e (blue) calculated using GRASP (Nicholls et al, 1991). (C) FRET-based competition assay. Emission profiles of 0.2 M BFP- IBB importin- and 0.2 M SV40 NLS-GFP without (red) 1 M Nup50 (residues 1-109) or with (black) 1 M Nup50 (residues 1-109, wild type) or with (blue) 1 M Nup50 (residues 1-109, K3E/R4D), or with (green) 1 M Nup50 (residues 1-109, R38A/R45D). (D) FRET-based competition assay. Emission profiles of 0.2 M BFP- IBB importin- and 0.2 M NP NLS-GFP without (red) 1 M Nup50 (residues 1-109) or with (black) 1 M Nup50 (residues 1-109, wild type) or with (blue) 1 M Nup50 (residues 1-109, K3E/R4D) or with (green) 1 M Nup50 (residues 1-109, R38A/R45D). 		Figure 5.
Figure 5 Nup50 (Nup2p) binds to sites crucial for the formation of nuclear export complex of importin- (Kap60p) with CAS (Cse1p) and RanGTP. (A) The Cse1p:Kap60p:RanGTP complex (Matsuura and Stewart, 2004). (B) Nup50 (red) and Nup2p (blue) are superimposed on the Kap60p ARM repeats in the Cse1p:Kap60p:RanGTP complex. (C) (A) and (B) superimposed. Cse1p, yellow; Ran, light blue; Kap60p IBB, pink; Kap60p ARM repeats, green. GTP is shown as space-filling model.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2005, 24, 3681-3689) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20960203 T.Merkle (2011).
Nucleo-cytoplasmic transport of proteins and RNA in plants.
  Plant Cell Rep, 30, 153-176.  
20335181 A.Giesecke, and M.Stewart (2010).
Novel binding of the mitotic regulator TPX2 (target protein for Xenopus kinesin-like protein 2) to importin-alpha.
  J Biol Chem, 285, 17628-17635.
PDB code: 3knd
20126445 A.Schmitz, A.Schwarz, M.Foss, L.Zhou, B.Rabe, J.Hoellenriegel, M.Stoeber, N.Panté, and M.Kann (2010).
Nucleoporin 153 arrests the nuclear import of hepatitis B virus capsids in the nuclear basket.
  PLoS Pathog, 6, e1000741.  
  21327077 H.Kosako, and N.Imamoto (2010).
Phosphorylation of nucleoporins: Signal transduction-mediated regulation of their interaction with nuclear transport receptors.
  Nucleus, 1, 309-313.  
20016008 Y.Ogawa, Y.Miyamoto, M.Asally, M.Oka, Y.Yasuda, and Y.Yoneda (2010).
Two isoforms of Npap60 (Nup50) differentially regulate nuclear protein import.
  Mol Biol Cell, 21, 630-638.  
19447185 C.Itman, Y.Miyamoto, J.Young, D.A.Jans, and K.L.Loveland (2009).
Nucleocytoplasmic transport as a driver of mammalian gametogenesis.
  Semin Cell Dev Biol, 20, 607-619.  
19767751 H.Kosako, N.Yamaguchi, C.Aranami, M.Ushiyama, S.Kose, N.Imamoto, H.Taniguchi, E.Nishida, and S.Hattori (2009).
Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport.
  Nat Struct Mol Biol, 16, 1026-1035.  
20514217 N.Freitas, and C.Cunha (2009).
Mechanisms and signals for the nuclear import of proteins.
  Curr Genomics, 10, 550-557.  
19809488 N.G.Ahn (2009).
PORE-ing over ERK substrates.
  Nat Struct Mol Biol, 16, 1004-1005.  
19465141 N.Yasuhara, M.Oka, and Y.Yoneda (2009).
The role of the nuclear transport system in cell differentiation.
  Semin Cell Dev Biol, 20, 590-599.  
19576221 S.A.Kennedy, M.L.Frazier, M.Steiniger, A.M.Mast, W.F.Marzluff, and M.R.Redinbo (2009).
Crystal structure of the HEAT domain from the Pre-mRNA processing factor Symplekin.
  J Mol Biol, 392, 115-128.
PDB code: 3gs3
18562297 C.Sun, W.Yang, L.C.Tu, and S.M.Musser (2008).
Single-molecule measurements of importin alpha/cargo complex dissociation at the nuclear pore.
  Proc Natl Acad Sci U S A, 105, 8613-8618.  
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.  
17682055 M.M.Pradeepa, S.Manjunatha, V.Sathish, S.Agrawal, and M.R.Rao (2008).
Involvement of importin-4 in the transport of transition protein 2 into the spermatid nucleus.
  Mol Cell Biol, 28, 4331-4341.  
17506639 A.Cook, F.Bono, M.Jinek, and E.Conti (2007).
Structural biology of nucleocytoplasmic transport.
  Annu Rev Biochem, 76, 647-671.  
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.  
17440484 C.P.Lusk, G.Blobel, and M.C.King (2007).
Highway to the inner nuclear membrane: rules for the road.
  Nat Rev Mol Cell Biol, 8, 414-420.  
17933776 M.A.Brykailo, L.M.McLane, J.Fridovich-Keil, and A.H.Corbett (2007).
Analysis of a predicted nuclear localization signal: implications for the intracellular localization and function of the Saccharomyces cerevisiae RNA-binding protein Scp160.
  Nucleic Acids Res, 35, 6862-6869.  
17851530 M.Beck, V.Lucić, F.Förster, W.Baumeister, and O.Medalia (2007).
Snapshots of nuclear pore complexes in action captured by cryo-electron tomography.
  Nature, 449, 611-615.  
17287812 M.Stewart (2007).
Molecular mechanism of the nuclear protein import cycle.
  Nat Rev Mol Cell Biol, 8, 195-208.  
17698002 T.A.Isgro, and K.Schulten (2007).
Cse1p-binding dynamics reveal a binding pattern for FG-repeat nucleoporins on transport receptors.
  Structure, 15, 977-991.  
16777596 E.J.Tran, and S.R.Wente (2006).
Dynamic nuclear pore complexes: life on the edge.
  Cell, 125, 1041-1053.  
16757945 M.F.Rexach (2006).
A sorting importin on Sec61.
  Nat Struct Mol Biol, 13, 476-478.  
16715095 S.Saksena, M.D.Summers, J.K.Burks, A.E.Johnson, and S.C.Braunagel (2006).
Importin-alpha-16 is a translocon-associated protein involved in sorting membrane proteins to the nuclear envelope.
  Nat Struct Mol Biol, 13, 500-508.  
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.

 

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