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PDBsum entry 1m5n

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protein Protein-protein interface(s) links
Protein transport PDB id
1m5n
Jmol PyMol
Contents
Protein chains
485 a.a. *
28 a.a. *
Waters ×37
* Residue conservation analysis
PDB id:
1m5n
Name: Protein transport
Title: Crystal structure of heat repeats (1-11) of importin b bound to the non-classical nls(67-94) of pthrp
Structure: Importin beta-1 subunit. Chain: s. Fragment: n-terminal domain (residues 1-485). Synonym: karyopherin beta-1 subunit, nuclear factor p97, importin 90. Engineered: yes. Parathyroid hormone-related protein. Chain: q. Fragment: residues 67-94.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in homo sapiens (human).
Biol. unit: Tetramer (from PQS)
Resolution:
2.90Å     R-factor:   0.250     R-free:   0.297
Authors: G.Cingolani,J.Bednenko,M.T.Gillespie,L.Gerace
Key ref:
G.Cingolani et al. (2002). Molecular basis for the recognition of a nonclassical nuclear localization signal by importin beta. Mol Cell, 10, 1345-1353. PubMed id: 12504010 DOI: 10.1016/S1097-2765(02)00727-X
Date:
09-Jul-02     Release date:   21-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q14974  (IMB1_HUMAN) -  Importin subunit beta-1
Seq:
Struc:
 
Seq:
Struc:
876 a.a.
485 a.a.
Protein chain
Pfam   ArchSchema ?
P12272  (PTHR_HUMAN) -  Parathyroid hormone-related protein
Seq:
Struc:
177 a.a.
28 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     intracellular protein transport   1 term 
  Biochemical function     hormone activity     2 terms  

 

 
DOI no: 10.1016/S1097-2765(02)00727-X Mol Cell 10:1345-1353 (2002)
PubMed id: 12504010  
 
 
Molecular basis for the recognition of a nonclassical nuclear localization signal by importin beta.
G.Cingolani, J.Bednenko, M.T.Gillespie, L.Gerace.
 
  ABSTRACT  
 
Nuclear import of proteins containing a classical nuclear localization signal (NLS) involves NLS recognition by importin alpha, which associates with importin beta via the IBB domain. Other proteins, including parathyroid hormone-related protein (PTHrP), are imported into the nucleus by direct interaction with importin beta. We solved the crystal structure of a fragment of importin beta-1 (1-485) bound to the nonclassical NLS of PTHrP. The structure reveals a second extended cargo binding site on importin beta distinct from the IBB domain binding site. Using a permeabilized cell import assay we demonstrate that importin beta (1-485) can import PTHrP-coupled cargo in a Ran-dependent manner. We propose that this region contains a prototypical nuclear import receptor domain, which could have evolved into the modern importin beta superfamily.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. NLS Sequences and Domain Structure of Importin β(A) Sequences of cNLSs, the IBB domain of importin α, and two ncNLSs from PTHrP and ribosomal protein L5 (BIB domain). The putative phosphorylation site (Thr85) of the PTHrP-ncNLS is in red.(B) Quantitative characterization of the binding of the PTHrP-ncNLS (67–94) to wild-type importin β and to two fragments of the protein spanning HEAT repeats 1–11 and 7–19, corresponding to residues 1–485 and 304–876, respectively. The apparent dissociation constants (K[d]) are shown.(C) Schematic domain organization of importin β. Each HEAT repeat is shown as two circles, corresponding to A and B helices. In green are the HEAT repeats cocrystallized with the PTHrP-ncNLS. The binding sites for the IBB domain, RanGTP, and nucleoporins are indicated by arrows.
Figure 5.
Figure 5. In Vitro Nuclear Import of BSA-PTHrP in Permeabilized HeLa CellsNuclear accumulation is observed in the presence of full-length importin β (HEAT 1–19) (A) and a fragment comprising HEAT 1–11 (C). No significant nuclear accumulation is observed in the absence of importin β (B) or using an importin β mutant (45–485) that does not bind Ran (D). Bar, 10 μM.
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2002, 10, 1345-1353) copyright 2002.  
  Figures were selected by an automated process.  

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
21182795 J.D.Nardozzi, K.Lott, and G.Cingolani (2010).
Phosphorylation meets nuclear import: a review.
  Cell Commun Signal, 8, 32.  
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
19939915 L.Riolobos, N.Valle, E.Hernando, B.Maroto, M.Kann, and J.M.Almendral (2010).
Viral oncolysis that targets Raf-1 signaling control of nuclear transport.
  J Virol, 84, 2090-2099.  
20471943 L.Song, and M.Rape (2010).
Regulated degradation of spindle assembly factors by the anaphase-promoting complex.
  Mol Cell, 38, 369-382.  
19801417 L.J.Terry, and S.R.Wente (2009).
Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport.
  Eukaryot Cell, 8, 1814-1827.  
19794817 R.B.Kopito, and M.Elbaum (2009).
Nucleocytoplasmic transport: a thermodynamic mechanism.
  HFSP J, 3, 130-141.  
19229862 Y.Miyauchi, N.Sakaguchi, T.Okada, M.Makishima, K.Ozono, and T.Michigami (2009).
Oncogenic nucleoporin CAN/Nup214 interacts with vitamin D receptor and modulates its function.
  J Cell Biochem, 106, 1090-1101.  
18343812 A.Lange, R.E.Mills, S.E.Devine, and A.H.Corbett (2008).
A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1.
  J Biol Chem, 283, 12926-12934.  
18187419 G.Mitrousis, A.S.Olia, N.Walker-Kopp, and G.Cingolani (2008).
Molecular basis for the recognition of snurportin 1 by importin beta.
  J Biol Chem, 283, 7877-7884.
PDB codes: 2p8q 2q5d
  18687138 M.D.Andrake, M.M.Sauter, K.Boland, A.D.Goldstein, M.Hussein, and A.M.Skalka (2008).
Nuclear import of Avian Sarcoma Virus integrase is facilitated by host cell factors.
  Retrovirology, 5, 73.  
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.  
  18541021 M.V.Nadella, S.T.Shu, W.P.Dirksen, N.K.Thudi, K.S.Nadella, S.A.Fernandez, M.D.Lairmore, P.L.Green, and T.J.Rosol (2008).
Expression of parathyroid hormone-related protein during immortalization of human peripheral blood mononuclear cells by HTLV-1: implications for transformation.
  Retrovirology, 5, 46.  
18366719 V.A.Delmar, R.C.Chan, and D.J.Forbes (2008).
Xenopus importin beta validates human importin beta as a cell cycle negative regulator.
  BMC Cell Biol, 9, 14.  
17506639 A.Cook, F.Bono, M.Jinek, and E.Conti (2007).
Structural biology of nucleocytoplasmic transport.
  Annu Rev Biochem, 76, 647-671.  
17548362 A.S.Philips, J.C.Kwok, and B.H.Chong (2007).
Analysis of the signals and mechanisms mediating nuclear trafficking of GATA-4. Loss of DNA binding is associated with localization in intranuclear speckles.
  J Biol Chem, 282, 24915-24927.  
18282135 A.V.Sorokin, E.R.Kim, and L.P.Ovchinnikov (2007).
Nucleocytoplasmic transport of proteins.
  Biochemistry (Mosc), 72, 1439-1457.  
17259172 D.Wohlwend, A.Strasser, A.Dickmanns, D.Doenecke, and R.Ficner (2007).
Thermodynamic analysis of H1 nuclear import: receptor tuning of importinbeta/importin7.
  J Biol Chem, 282, 10707-10719.  
17287812 M.Stewart (2007).
Molecular mechanism of the nuclear protein import cycle.
  Nat Rev Mol Cell Biol, 8, 195-208.  
17938174 S.Neimanis, W.Albig, D.Doenecke, and J.Kahle (2007).
Sequence elements in both subunits of the DNA fragmentation factor are essential for its nuclear transport.
  J Biol Chem, 282, 35821-35830.  
17485461 T.Fries, C.Betz, K.Sohn, S.Caesar, G.Schlenstedt, and S.M.Bailer (2007).
A novel conserved nuclear localization signal is recognized by a group of yeast importins.
  J Biol Chem, 282, 19292-19301.  
16551631 A.Dittmer, M.Vetter, D.Schunke, P.N.Span, F.Sweep, C.Thomssen, and J.Dittmer (2006).
Parathyroid hormone-related protein regulates tumor-relevant genes in breast cancer cells.
  J Biol Chem, 281, 14563-14572.  
16421734 A.S.Madrid, and K.Weis (2006).
Nuclear transport is becoming crystal clear.
  Chromosoma, 115, 98.  
16901787 B.J.Lee, A.E.Cansizoglu, K.E.Süel, T.H.Louis, Z.Zhang, and Y.M.Chook (2006).
Rules for nuclear localization sequence recognition by karyopherin beta 2.
  Cell, 126, 543-558.
PDB code: 2h4m
16567089 E.Conti, C.W.Müller, and M.Stewart (2006).
Karyopherin flexibility in nucleocytoplasmic transport.
  Curr Opin Struct Biol, 16, 237-244.  
16552725 H.W.Lo, M.Ali-Seyed, Y.Wu, G.Bartholomeusz, S.C.Hsu, and M.C.Hung (2006).
Nuclear-cytoplasmic transport of EGFR involves receptor endocytosis, importin beta1 and CRM1.
  J Cell Biochem, 98, 1570-1583.  
16973564 H.Wodrich, A.Cassany, M.A.D'Angelo, T.Guan, G.Nemerow, and L.Gerace (2006).
Adenovirus core protein pVII is translocated into the nucleus by multiple import receptor pathways.
  J Virol, 80, 9608-9618.  
16240320 H.Yagisawa (2006).
Nucleocytoplasmic shuttling of phospholipase C-delta1: a link to Ca2+.
  J Cell Biochem, 97, 233-243.  
17035634 L.Goffin, S.Vodala, C.Fraser, J.Ryan, M.Timms, S.Meusburger, B.Catimel, E.C.Nice, P.A.Silver, C.Y.Xiao, D.A.Jans, and M.J.Gething (2006).
The unfolded protein response transducer Ire1p contains a nuclear localization sequence recognized by multiple beta importins.
  Mol Biol Cell, 17, 5309-5323.  
16525863 M.A.van der Aa, E.Mastrobattista, R.S.Oosting, W.E.Hennink, G.A.Koning, and D.J.Crommelin (2006).
The nuclear pore complex: the gateway to successful nonviral gene delivery.
  Pharm Res, 23, 447-459.  
16407315 M.Arnold, A.Nath, D.Wohlwend, and R.H.Kehlenbach (2006).
Transportin is a major nuclear import receptor for c-Fos: a novel mode of cargo interaction.
  J Biol Chem, 281, 5492-5499.  
16704975 M.Arnold, A.Nath, J.Hauber, and R.H.Kehlenbach (2006).
Multiple importins function as nuclear transport receptors for the Rev protein of human immunodeficiency virus type 1.
  J Biol Chem, 281, 20883-20890.  
  16880557 T.Imasaki, T.Shimizu, H.Hashimoto, Y.Hidaka, M.Yamada, and M.Sato (2006).
Crystallization and preliminary X-ray crystallographic studies of transportin 1 in complex with nucleocytoplasmic shuttling and nuclear localization fragments.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 785-787.  
16962977 U.Zachariae, and H.Grubmüller (2006).
A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations.
  Structure, 14, 1469-1478.  
16176272 D.R.Littler, N.N.Assaad, S.J.Harrop, L.J.Brown, G.J.Pankhurst, P.Luciani, M.I.Aguilar, M.Mazzanti, M.A.Berryman, S.N.Breit, and P.M.Curmi (2005).
Crystal structure of the soluble form of the redox-regulated chloride ion channel protein CLIC4.
  FEBS J, 272, 4996-5007.
PDB code: 2ahe
15880121 H.Viadiu, O.Stemmann, M.W.Kirschner, and T.Walz (2005).
Domain structure of separase and its binding to securin as determined by EM.
  Nat Struct Mol Biol, 12, 552-553.  
15702987 L.F.Pemberton, and B.M.Paschal (2005).
Mechanisms of receptor-mediated nuclear import and nuclear export.
  Traffic, 6, 187-198.  
15611084 M.H.Chen, I.Ben-Efraim, G.Mitrousis, N.Walker-Kopp, P.J.Sims, and G.Cingolani (2005).
Phospholipid scramblase 1 contains a nonclassical nuclear localization signal with unique binding site in importin alpha.
  J Biol Chem, 280, 10599-10606.
PDB code: 1y2a
15864302 S.J.Lee, Y.Matsuura, S.M.Liu, and M.Stewart (2005).
Structural basis for nuclear import complex dissociation by RanGTP.
  Nature, 435, 693-696.
PDB code: 2bku
15525506 A.Harel, and D.J.Forbes (2004).
Importin beta: conducting a much larger cellular symphony.
  Mol Cell, 16, 319-330.  
14730349 C.C.Milburn, J.Boudeau, M.Deak, D.R.Alessi, and D.M.van Aalten (2004).
Crystal structure of MO25 alpha in complex with the C terminus of the pseudo kinase STE20-related adaptor.
  Nat Struct Mol Biol, 11, 193-200.
PDB codes: 1upk 1upl
15574331 C.Petosa, G.Schoehn, P.Askjaer, U.Bauer, M.Moulin, U.Steuerwald, M.Soler-López, F.Baudin, I.W.Mattaj, and C.W.Müller (2004).
Architecture of CRM1/Exportin1 suggests how cooperativity is achieved during formation of a nuclear export complex.
  Mol Cell, 16, 761-775.
PDB code: 1w9c
15367670 D.M.Leslie, W.Zhang, B.L.Timney, B.T.Chait, M.P.Rout, R.W.Wozniak, and J.D.Aitchison (2004).
Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import.
  Mol Cell Biol, 24, 8487-8503.  
14561738 N.Fukuhara, E.Fernandez, J.Ebert, E.Conti, and D.Svergun (2004).
Conformational variability of nucleo-cytoplasmic transport factors.
  J Biol Chem, 279, 2176-2181.  
15450977 N.Mosammaparast, and L.F.Pemberton (2004).
Karyopherins: from nuclear-transport mediators to nuclear-function regulators.
  Trends Cell Biol, 14, 547-556.  
12594203 C.Koerner, T.Guan, L.Gerace, and G.Cingolani (2003).
Synergy of silent and hot spot mutations in importin beta reveals a dynamic mechanism for recognition of a nuclear localization signal.
  J Biol Chem, 278, 16216-16221.  
12490886 E.Conti (2003).
The hitchhiker's guide to the nucleus.
  Nat Struct Biol, 10, 8-9.  
12885761 J.Bednenko, G.Cingolani, and L.Gerace (2003).
Importin beta contains a COOH-terminal nucleoporin binding region important for nuclear transport.
  J Cell Biol, 162, 391-401.  
14645832 M.Stewart (2003).
Structural biology. Nuclear trafficking.
  Science, 302, 1513-1514.  
14501140 S.J.Lee, T.Sekimoto, E.Yamashita, E.Nagoshi, A.Nakagawa, H.Tanaka, Y.Yoneda, and T.Tsukihara (2003).
Crystallization and preliminary crystallographic analysis of the importin-beta-SREBP-2 complex.
  Acta Crystallogr D Biol Crystallogr, 59, 1866-1868.  
14645851 S.J.Lee, T.Sekimoto, E.Yamashita, E.Nagoshi, A.Nakagawa, N.Imamoto, M.Yoshimura, H.Sakai, K.T.Chong, T.Tsukihara, and Y.Yoneda (2003).
The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor.
  Science, 302, 1571-1575.
PDB code: 1ukl
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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