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PDBsum entry 2bku

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protein ligands metals Protein-protein interface(s) links
Nuclear transport PDB id
2bku
Jmol
Contents
Protein chains
169 a.a. *
857 a.a. *
Ligands
GTP ×2
Metals
_MG ×2
Waters ×62
* Residue conservation analysis
PDB id:
2bku
Name: Nuclear transport
Title: Kap95p:rangtp complex
Structure: Gtp-binding nuclear protein ran. Chain: a, c. Fragment: residues 1-177. Synonym: gtpase ran, ras-like protein tc4. Engineered: yes. Importin beta-1 subunit. Chain: b, d. Synonym: karyopherin beta-1 subunit, importin 95. Engineered: yes
Source: Canis familiaris. Dog. Organism_taxid: 9615. Expressed in: escherichia coli. Expression_system_taxid: 562. Saccharomyces cerevisiae. Bakers yeast. Organism_taxid: 4932. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.70Å     R-factor:   0.226     R-free:   0.279
Authors: S.J.Lee,Y.Matsuura,S.M.Liu,M.Stewart
Key ref:
S.J.Lee et al. (2005). Structural basis for nuclear import complex dissociation by RanGTP. Nature, 435, 693-696. PubMed id: 15864302 DOI: 10.1038/nature03578
Date:
21-Feb-05     Release date:   04-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P62825  (RAN_CANFA) -  GTP-binding nuclear protein Ran
Seq:
Struc:
216 a.a.
169 a.a.*
Protein chains
Pfam   ArchSchema ?
Q06142  (IMB1_YEAST) -  Importin subunit beta-1
Seq:
Struc:
 
Seq:
Struc:
861 a.a.
857 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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

 

 
DOI no: 10.1038/nature03578 Nature 435:693-696 (2005)
PubMed id: 15864302  
 
 
Structural basis for nuclear import complex dissociation by RanGTP.
S.J.Lee, Y.Matsuura, S.M.Liu, M.Stewart.
 
  ABSTRACT  
 
Nuclear protein import is mediated mainly by the transport factor importin-beta that binds cytoplasmic cargo, most often via the importin-alpha adaptor, and then transports it through nuclear pore complexes. This active transport is driven by disassembly of the import complex by nuclear RanGTP. The switch I and II loops of Ran change conformation with nucleotide state, and regulate its interactions with nuclear trafficking components. Importin-beta consists of 19 HEAT repeats that are based on a pair of antiparallel alpha-helices (referred to as the A- and B-helices). The HEAT repeats stack to yield two C-shaped arches, linked together to form a helicoidal molecule that has considerable conformational flexibility. Here we present the structure of full-length yeast importin-beta (Kap95p or karyopherin-beta) complexed with RanGTP, which provides a basis for understanding the crucial cargo-release step of nuclear import. We identify a key interaction site where the RanGTP switch I loop binds to the carboxy-terminal arch of Kap95p. This interaction produces a change in helicoidal pitch that locks Kap95p in a conformation that cannot bind importin-alpha or cargo. We suggest an allosteric mechanism for nuclear import complex disassembly by RanGTP.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structure of the Kap95p -RanGTP complex. a, Two views of the Kap95p -RanGTP complex, rotated by 90 relative to one another. Kap95p is shown in yellow and the main-chain trace of RanGTP is shown in dark blue, with the switch I loop in red and the switch II loop in green. The bound GTP is shown in space-filling format. b, Schematic illustration of the residues interacting at each site. The CRIME motif in HEAT repeats (H)1 -4 of Kap95p interacts primarily with the switch II loop of RanGTP, and the basic patch on RanGTP binds mainly to the acidic loop in HEAT repeat 8. The third interaction site primarily involves interactions between the switch I loop (red) and residues in HEAT repeats 12 -15. c, Details of the interaction site in the Kap95p C-terminal arch (yellow) that involves the Ran switch I loop (red) and Ran residues 151 -158 (blue). Lys 37 and Lys 152 of Ran make salt bridges with acidic residues from HEAT repeat 14; Arg 29^Ran, Asn 154^Ran and Asn 156^Ran form an extensive hydrogen-bonded network; and Phe 35^Ran and Phe 157^Ran, together with Phe 613 and Leu 563 of Kap95p, are also buried. d, Stereo view showing the conformational changes between Kap95p bound to different partners, IBB (red), SREBP-2 (cyan) and RanGTP (yellow), indicative of considerable molecular flexibility. The centres of consecutive HEAT repeats in each Kap95p molecule are represented by spheres. RanGTP binding locks Kap95p into a conformation with a higher helicoidal pitch that is incompatible with binding nuclear import partners. e, Schematic illustration of an unzipping mechanism by which RanGTP might displace the IBB domain from Kap95p. Kap95p is shown in yellow, and RanGTP in blue. An extended section of the L-shaped IBB domain (black) binds Kap95p HEAT repeats 7 -11, while an -helical segment binds HEAT repeats 12 -19. RanGTP binds initially to the CRIME domain at the Kap95p N terminus and then displaces the extended IBB region by binding to the acidic loop in HEAT repeat 8. RanGTP binding to the additional site in the C-terminal arch then increases the helicoidal pitch of Kap95p, resulting in a mismatch between it and the IBB domain helix, which is then released.
Figure 2.
Figure 2: RanGTP with K37D/K152A mutations binds Kap95p and importin- beta-but does not displace the IBB domain. a, Although both Kap95p and human importin- only bind weakly to wild-type (WT) RanGDP, they bind K37D/K152A-RanGTP, Q69L-RanGTP and WT RanGTP with comparable affinity. b, The amount of Kap95p and human importin- bound to GST-IBB depends on the state of the nucleotide bound to Ran. Kap95p and importin- remain bound in the presence of RanGDP, but are displaced by RanGTP and Q69L-RanGTP. However, Kap95p and importin- are displaced much less efficiently by the GTP-bound form of the Ran K37D/K152A mutant, which disrupts the interaction at the additional Ran-binding site in the C-terminal arch of Kap95p (Fig. 1c).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 435, 693-696) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20649471 J.Heo (2011).
Redox control of GTPases: from molecular mechanisms to functional significance in health and disease.
  Antioxid Redox Signal, 14, 689-724.  
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.  
20028483 A.Lange, L.M.McLane, R.E.Mills, S.E.Devine, and A.H.Corbett (2010).
Expanding the definition of the classical bipartite nuclear localization signal.
  Traffic, 11, 311-323.  
20148114 C.Shoubridge, M.H.Tan, T.Fullston, D.Cloosterman, D.Coman, G.McGillivray, G.M.Mancini, T.Kleefstra, and J.Gécz (2010).
Mutations in the nuclear localization sequence of the Aristaless related homeobox; sequestration of mutant ARX with IPO13 disrupts normal subcellular distribution of the transcription factor and retards cell division.
  Pathogenetics, 3, 1.  
20506206 C.Shoubridge, T.Fullston, and J.Gécz (2010).
ARX spectrum disorders: making inroads into the molecular pathology.
  Hum Mutat, 31, 889-900.  
20875127 G.Zhou, C.L.Doçi, and M.W.Lingen (2010).
Identification and functional analysis of NOL7 nuclear and nucleolar localization signals.
  BMC Cell Biol, 11, 74.  
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
20368455 J.Ma, and W.Yang (2010).
Three-dimensional distribution of transient interactions in the nuclear pore complex obtained from single-molecule snapshots.
  Proc Natl Acad Sci U S A, 107, 7305-7310.  
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
19737937 A.Monette, L.Ajamian, M.López-Lastra, and A.J.Mouland (2009).
Human immunodeficiency virus type 1 (HIV-1) induces the cytoplasmic retention of heterogeneous nuclear ribonucleoprotein A1 by disrupting nuclear import: implications for HIV-1 gene expression.
  J Biol Chem, 284, 31350-31362.  
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
19308634 D.A.Mason, D.E.Stage, and D.S.Goldfarb (2009).
Evolution of the metazoan-specific importin alpha gene family.
  J Mol Evol, 68, 351-365.  
19124778 J.C.Phillips (2009).
Scaling and self-organized criticality in proteins II.
  Proc Natl Acad Sci U S A, 106, 3113-3118.  
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.  
19514019 L.M.McLane, and A.H.Corbett (2009).
Nuclear localization signals and human disease.
  IUBMB Life, 61, 697-706.  
20514217 N.Freitas, and C.Cunha (2009).
Mechanisms and signals for the nuclear import of proteins.
  Curr Genomics, 10, 550-557.  
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
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
18727838 R.Mosca, B.Brannetti, and T.R.Schneider (2008).
Alignment of protein structures in the presence of domain motions.
  BMC Bioinformatics, 9, 352.  
18845677 S.Otsuka, S.Iwasaka, Y.Yoneda, K.Takeyasu, and S.H.Yoshimura (2008).
Individual binding pockets of importin-beta for FG-nucleoporins have different binding properties and different sensitivities to RanGTP.
  Proc Natl Acad Sci U S A, 105, 16101-16106.  
18547523 U.Zachariae, and H.Grubmüller (2008).
Importin-beta: structural and dynamic determinants of a molecular spring.
  Structure, 16, 906-915.  
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.  
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.  
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.  
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.  
17984325 I.I.Rybkin, M.S.Kim, S.Bezprozvannaya, X.Qi, J.A.Richardson, C.F.Plato, J.A.Hill, R.Bassel-Duby, and E.N.Olson (2007).
Regulation of atrial natriuretic peptide secretion by a novel Ras-like protein.
  J Cell Biol, 179, 527-537.  
17182855 K.J.Ryan, Y.Zhou, and S.R.Wente (2007).
The karyopherin Kap95 regulates nuclear pore complex assembly into intact nuclear envelopes in vivo.
  Mol Biol Cell, 18, 886-898.  
17287812 M.Stewart (2007).
Molecular mechanism of the nuclear protein import cycle.
  Nat Rev Mol Cell Biol, 8, 195-208.  
17646647 R.B.Kopito, and M.Elbaum (2007).
Reversibility in nucleocytoplasmic transport.
  Proc Natl Acad Sci U S A, 104, 12743-12748.  
17240517 R.Truant, R.S.Atwal, and A.Burtnik (2007).
Nucleocytoplasmic trafficking and transcription effects of huntingtin in Huntington's disease.
  Prog Neurobiol, 83, 211-227.  
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.  
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.  
  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.  
16338415 T.A.Isgro, and K.Schulten (2005).
Binding dynamics of isolated nucleoporin repeat regions to importin-beta.
  Structure, 13, 1869-1879.  
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 code is shown on the right.