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PDBsum entry 1wa5

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protein ligands metals Protein-protein interface(s) links
Nuclear transport PDB id
1wa5
Jmol
Contents
Protein chains
170 a.a. *
464 a.a. *
938 a.a. *
Ligands
GTP
Metals
_MG
Waters ×472
* Residue conservation analysis
PDB id:
1wa5
Name: Nuclear transport
Title: Crystal structure of the exportin cse1p complexed with its cargo (kap60p) and rangtp
Structure: Gtp-binding nuclear protein ran. Chain: a. Fragment: residues 1-176. Synonym: gtpase ran, ras-like protein tc4. Engineered: yes. Importin alpha re-exporter. Chain: c. Synonym: chromosome segregation protein cse1, cse1p. Engineered: yes.
Source: Canis familiaris. Dog. Organism_taxid: 9615. Expressed in: escherichia coli. Expression_system_taxid: 469008. Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932.
Biol. unit: Trimer (from PDB file)
Resolution:
2.00Å     R-factor:   0.234     R-free:   0.267
Authors: Y.Matsuura,M.Stewart
Key ref:
Y.Matsuura and M.Stewart (2004). Structural basis for the assembly of a nuclear export complex. Nature, 432, 872-877. PubMed id: 15602554 DOI: 10.1038/nature03144
Date:
23-Oct-04     Release date:   13-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62825  (RAN_CANFA) -  GTP-binding nuclear protein Ran
Seq:
Struc:
216 a.a.
170 a.a.
Protein chain
Pfam   ArchSchema ?
Q02821  (IMA1_YEAST) -  Importin subunit alpha
Seq:
Struc:
 
Seq:
Struc:
542 a.a.
464 a.a.
Protein chain
Pfam   ArchSchema ?
P33307  (CSE1_YEAST) -  Importin alpha re-exporter
Seq:
Struc:
 
Seq:
Struc:
960 a.a.
938 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   5 terms 
  Biological process     cell cycle   13 terms 
  Biochemical function     protein binding     6 terms  

 

 
DOI no: 10.1038/nature03144 Nature 432:872-877 (2004)
PubMed id: 15602554  
 
 
Structural basis for the assembly of a nuclear export complex.
Y.Matsuura, M.Stewart.
 
  ABSTRACT  
 
The nuclear import and export of macromolecular cargoes through nuclear pore complexes is mediated primarily by carriers such as importin-beta. Importins carry cargoes into the nucleus, whereas exportins carry cargoes to the cytoplasm. Transport is orchestrated by nuclear RanGTP, which dissociates cargoes from importins, but conversely is required for cargo binding to exportins. Here we present the 2.0 A crystal structure of the nuclear export complex formed by exportin Cse1p complexed with its cargo (Kap60p) and RanGTP, thereby providing a structural framework for understanding nuclear protein export and the different functions of RanGTP in export and import. In the complex, Cse1p coils around both RanGTP and Kap60p, stabilizing the RanGTP-state and clamping the Kap60p importin-beta-binding domain, ensuring that only cargo-free Kap60p is exported. Mutagenesis indicated that conformational changes in exportins couple cargo binding to high affinity for RanGTP, generating a spring-loaded molecule to facilitate disassembly of the export complex following GTP hydrolysis in the cytoplasm.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Two orthogonal views, showing an overview of the structure of the Cse1p:Kap60p:RanGTP complex. The figure illustrates how Cse1p (yellow) envelopes RanGTP (blue), and the C-terminal region of Kap60p (green) and its IBB domain (magenta). The Cse1p -helices are represented by cylinders, whereas the HEAT8 insert and HEAT19 loop are highlighted in pink and orange, respectively. The ARM repeats of Kap60p and HEAT repeats of Cse1p are labelled A1 -A10 and H1 -H20, respectively. GTP is shown as spacefilling spheres. Key residues mentioned in the text are shown in ball-and-stick representation.
Figure 3.
Figure 3: Role of Ran in the export complex. a, Interfaces between Cse1p (yellow) and Ran (switch I, magenta; switch II, orange). Ran Arg 76 and Asp 77 in the switch II loop are key components of the Cse1p N-interface, whereas Lys 37 (switch I loop) and Lys 152 bind the C-interface. An omit-annealed F[o] -F[c] map around GTP at 3.5 is superimposed, confirming the nucleotide state. b, Ran Arg 95, Lys 99, Lys 130 and Lys 134 are key components of the interface between RanGTP (blue) and Kap60p (green). c, Docking RanBD1 onto the Cse1p:Kap60p:RanGTP complex shows a steric clash between Cse1p and the RanGTP C terminus. The coordinates of Ran bound to RanBD1 (red) were superimposed with Ran (residues 1 -176) in the Cse1p:Kap60p:RanGTP complex. C-terminal residues of Ran (176 -210) in the Ran-RanBD1 complex, dark blue; other colour coding as Fig. 1. d, Model for Cse1p:Kap60p:RanGTP complex assembly. Dotted lines represent interactions. In the absence of Kap60p, Cse1p has a lower-energy conformation that binds Ran at only one site. When Kap60p binds, Cse1p is distorted into a higher-energy state that allows Ran to bind to the second site, generating a spring-loaded complex that would disassemble spontaneously on RanGTP hydrolysis. The representation of Cse1p here is highly schematic, and is intended only to imply a conformational change and not the precise structure of either state.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2004, 432, 872-877) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22343721 A.M.Ellisdon, L.Dimitrova, E.Hurt, and M.Stewart (2012).
Structural basis for the assembly and nucleic acid binding of the TREX-2 transcription-export complex.
  Nat Struct Mol Biol, 19, 328-336.
PDB codes: 3t5v 3t5x
21145229 S.J.Lee, C.Jiko, E.Yamashita, and T.Tsukihara (2011).
Selective nuclear export mechanism of small RNAs.
  Curr Opin Struct Biol, 21, 101-108.  
21315084 T.Ito, A.Narita, T.Hirayama, M.Taki, S.Iyoshi, Y.Yamamoto, Y.Maéda, and T.Oda (2011).
Human spire interacts with the barbed end of the actin filament.
  J Mol Biol, 408, 18-25.  
21478864 T.T.Nguyen, S.C.Chang, I.Evnouchidou, I.A.York, C.Zikos, K.L.Rock, A.L.Goldberg, E.Stratikos, and L.J.Stern (2011).
Structural basis for antigenic peptide precursor processing by the endoplasmic reticulum aminopeptidase ERAP1.
  Nat Struct Mol Biol, 18, 604-613.
PDB code: 3mdj
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
20007317 A.M.Ellisdon, D.Jani, A.Köhler, E.Hurt, and M.Stewart (2010).
Structural basis for the interaction between yeast Spt-Ada-Gcn5 acetyltransferase (SAGA) complex components Sgf11 and Sus1.
  J Biol Chem, 285, 3850-3856.
PDB codes: 3kik 3kjl
20463024 C.Zheng, M.B.Fasken, N.J.Marshall, C.Brockmann, M.E.Rubinson, S.R.Wente, A.H.Corbett, and M.Stewart (2010).
Structural basis for the function of the Saccharomyces cerevisiae Gfd1 protein in mRNA nuclear export.
  J Biol Chem, 285, 20704-20715.
PDB code: 3lcn
20543818 J.E.Braun, F.Tritschler, G.Haas, C.Igreja, V.Truffault, O.Weichenrieder, and E.Izaurralde (2010).
The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa.
  EMBO J, 29, 2368-2380.
PDB codes: 2xeq 2xer 2xes
20554526 S.M.Kelly, S.W.Leung, L.H.Apponi, A.M.Bramley, E.J.Tran, J.A.Chekanova, S.R.Wente, and A.H.Corbett (2010).
Recognition of polyadenosine RNA by the zinc finger domain of nuclear poly(A) RNA-binding protein 2 (Nab2) is required for correct mRNA 3'-end formation.
  J Biol Chem, 285, 26022-26032.  
20972448 T.Güttler, T.Madl, P.Neumann, D.Deichsel, L.Corsini, T.Monecke, R.Ficner, M.Sattler, and D.Görlich (2010).
NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.
  Nat Struct Mol Biol, 17, 1367-1376.
PDB codes: 2l1l 3nby 3nbz 3nc0 3nc1
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.  
19680239 A.G.Cook, N.Fukuhara, M.Jinek, and E.Conti (2009).
Structures of the tRNA export factor in the nuclear and cytosolic states.
  Nature, 461, 60-65.
PDB codes: 3ibv 3icq
19965479 C.Okada, E.Yamashita, S.J.Lee, S.Shibata, J.Katahira, A.Nakagawa, Y.Yoneda, and T.Tsukihara (2009).
A High-Resolution Structure of the Pre-microRNA Nuclear Export Machinery.
  Science, 326, 1275-1279.
PDB code: 3a6p
19328066 D.Jani, S.Lutz, N.J.Marshall, T.Fischer, A.Köhler, A.M.Ellisdon, E.Hurt, and M.Stewart (2009).
Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export.
  Mol Cell, 33, 727-737.
PDB codes: 3fwb 3fwc
19421156 E.W.Debler, G.Blobel, and A.Hoelz (2009).
Nuclear transport comes full circle.
  Nat Struct Mol Biol, 16, 457-459.  
19282972 G.A.Palidwor, S.Shcherbinin, M.R.Huska, T.Rasko, U.Stelzl, A.Arumughan, R.Foulle, P.Porras, L.Sanchez-Pulido, E.E.Wanker, and M.A.Andrade-Navarro (2009).
Detection of alpha-rod protein repeats using a neural network and application to huntingtin.
  PLoS Comput Biol, 5, e1000304.  
19124778 J.C.Phillips (2009).
Scaling and self-organized criticality in proteins II.
  Proc Natl Acad Sci U S A, 106, 3113-3118.  
19505478 J.R.Partridge, and T.U.Schwartz (2009).
Crystallographic and biochemical analysis of the Ran-binding zinc finger domain.
  J Mol Biol, 391, 375-389.
PDB codes: 3gj0 3gj3 3gj4 3gj5 3gj6 3gj7 3gj8
18984568 K.F.Pulliam, M.B.Fasken, L.M.McLane, J.V.Pulliam, and A.H.Corbett (2009).
The Classical Nuclear Localization Signal Receptor, Importin-{alpha}, Is Required for Efficient Transition Through the G1/S Stage of the Cell Cycle in Saccharomyces cerevisiae.
  Genetics, 181, 105-118.  
20041180 M.Kodiha, D.Tran, A.Morogan, C.Qian, and U.Stochaj (2009).
Dissecting the signaling events that impact classical nuclear import and target nuclear transport factors.
  PLoS One, 4, e8420.  
19274657 R.Peters (2009).
Translocation through the nuclear pore: Kaps pave the way.
  Bioessays, 31, 466-477.  
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.  
18190927 R.P.Grant, N.J.Marshall, J.C.Yang, M.B.Fasken, S.M.Kelly, M.T.Harreman, D.Neuhaus, A.H.Corbett, and M.Stewart (2008).
Structure of the N-terminal Mlp1-binding domain of the Saccharomyces cerevisiae mRNA-binding protein, Nab2.
  J Mol Biol, 376, 1048-1059.
PDB codes: 2jps 2v75
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.  
17461799 C.P.Lusk, D.D.Waller, T.Makhnevych, A.Dienemann, M.Whiteway, D.Y.Thomas, and R.W.Wozniak (2007).
Nup53p is a target of two mitotic kinases, Cdk1p and Hrr25p.
  Traffic, 8, 647-660.  
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.  
17082180 P.Kowal, A.M.Gurtan, P.Stuckert, A.D.D'Andrea, and T.Ellenberger (2007).
Structural determinants of human FANCF protein that function in the assembly of a DNA damage signaling complex.
  J Biol Chem, 282, 2047-2055.
PDB code: 2iqc
17465889 S.Shilo, S.Roy, S.Khanna, and C.K.Sen (2007).
MicroRNA in cutaneous wound healing: a new paradigm.
  DNA Cell Biol, 26, 227-237.  
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.  
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.  
17719542 T.Tanaka, S.Ohkubo, I.Tatsuno, and C.Prives (2007).
hCAS/CSE1L associates with chromatin and regulates expression of select p53 target genes.
  Cell, 130, 638-650.  
16785238 A.E.Hodel, M.T.Harreman, K.F.Pulliam, M.E.Harben, J.S.Holmes, M.R.Hodel, K.M.Berland, and A.H.Corbett (2006).
Nuclear localization signal receptor affinity correlates with in vivo localization in Saccharomyces cerevisiae.
  J Biol Chem, 281, 23545-23556.  
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.  
16777596 E.J.Tran, and S.R.Wente (2006).
Dynamic nuclear pore complexes: life on the edge.
  Cell, 125, 1041-1053.  
16637892 L.F.Pemberton, and B.M.Paschal (2006).
Scientists share nuclear secrets at Jekyll Island.
  Traffic, 7, 751-760.  
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.  
15702987 L.F.Pemberton, and B.M.Paschal (2005).
Mechanisms of receptor-mediated nuclear import and nuclear export.
  Traffic, 6, 187-198.  
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
16222336 Y.Matsuura, and M.Stewart (2005).
Nup50/Npap60 function in nuclear protein import complex disassembly and importin recycling.
  EMBO J, 24, 3681-3689.
PDB codes: 2c1m 2c1t
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.