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PDBsum entry 1gcj
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Transport protein
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PDB id
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1gcj
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Contents |
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* Residue conservation analysis
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PDB id:
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Transport protein
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Title:
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N-terminal fragment of importin-beta
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Structure:
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Importin beta. Chain: a, b. Fragment: n-terminal domain (1-449 residues). Engineered: yes. Mutation: yes
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Source:
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Mus musculus. House mouse. Organism_taxid: 10090. Strain: c57bl6. Tissue: thymus. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Dimer (from
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Resolution:
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2.60Å
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R-factor:
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0.215
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R-free:
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0.270
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Authors:
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S.J.Lee,N.Imamoto,H.Sakai,A.Nakagawa,S.Kose,M.Koike,M.Yamamoto, T.Kumasaka,Y.Yoneda,T.Tsukihara
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Key ref:
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S.J.Lee
et al.
(2000).
The adoption of a twisted structure of importin-beta is essential for the protein-protein interaction required for nuclear transport.
J Mol Biol,
302,
251-264.
PubMed id:
DOI:
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Date:
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31-Jul-00
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Release date:
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18-Oct-00
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PROCHECK
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Headers
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References
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P70168
(IMB1_MOUSE) -
Importin subunit beta-1 from Mus musculus
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Seq:
Struc:
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876 a.a.
460 a.a.*
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Key: |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 4 residue positions (black
crosses)
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DOI no:
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J Mol Biol
302:251-264
(2000)
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PubMed id:
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The adoption of a twisted structure of importin-beta is essential for the protein-protein interaction required for nuclear transport.
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S.J.Lee,
N.Imamoto,
H.Sakai,
A.Nakagawa,
S.Kose,
M.Koike,
M.Yamamoto,
T.Kumasaka,
Y.Yoneda,
T.Tsukihara.
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ABSTRACT
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Importin-beta is a nuclear transport factor which mediates the nuclear import of
various nuclear proteins. The N-terminal 1-449 residue fragment of mouse
importin-beta (impbeta449) possesses the ability to bidirectionally translocate
through the nuclear pore complex (NPC), and to bind RanGTP. The structure of the
uncomplexed form of impbeta449 has been solved at a 2.6 A resolution by X-ray
crystallography. It consists of ten copies of the tandemly arrayed HEAT repeat
and exhibits conformational flexibility which is involved in protein-protein
interaction for nuclear transport. The overall conformation of the HEAT repeats
shows that a twisted motion produces a significantly varied superhelical
architecture from the previously reported structure of RanGTP-bound
importin-beta. These conformational changes appear to be the sum of small
conformational changes throughout the polypeptide. Such a flexibility, which
resides in the stacked HEAT repeats, is essential for interaction with RanGTP or
with NPCs. Furthermore, it was found that impbeta449 has a structural similarity
with another nuclear migrating protein, namely beta-catenin, which is composed
of another type of helix-repeated structure of ARM repeat. Interestingly, the
essential regions for NPC translocation for both importin-beta and beta-catenin
are spatially well overlapped with one another. This strongly indicates the
importance of helix stacking of the HEAT or ARM repeats for NPC-passage.
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Selected figure(s)
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Figure 1.
Figure 1. Structure of impb449. (a) Stereo view of impb449
dimer in the asymmetric unit. The crystal structure of the
impb449 molecules forms a dimer, which is composed of molecule
I(pink) and II(green) in the asymmetric unit. Three interaction
sites for dimer formation are depicted by the ball-and-stick
model. The C-terminal area interaction is in purple, and the
second and third interaction sites are in blue and red,
respectively. (b) HEAT repeat helices in impb449. The convex
side of helices of A1-A10 and the concave side of the helices of
B1-B10 and 3[10] helices are colored in blue, red and light
blue, respectively. C2 helix is colored in green. (c) Structural
alignment of the ten HEAT repeats of impb449. The first amino
acid residue of each repeat is indicated on the left. Each
repeat contains helix A and B. The repeat 2 contains helix C.
Underlined residues in repeats 3, 4, and 5 comprise 3[10]
helices indicated in (b).
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Figure 4.
Figure 4. Hypothetically constructed superhelix structures
of three importin-bs. HEAT repeat helices from A3 to B9, stacked
side-by-side, are superposed. The residues of amino acid
residues 1-449 are used for the construction of the superhelix.
One pitch of superhelix is comprised of 24 molecules (impb449),
23 molecules (impb/IBB) and 23 molecules (impb/Ran),
respectively. Left, superhelix of impb449 (monomerI:uncomplexed
form); middle, superhelix of impb/IBB (PDB code 1QGK:RanGTP
uncomplexed form, but complexed with IBB in the C terminal half
of full length of importin-b); right, superhelix of impb/Ran
(PDB code 1IBR, chain B:RanGTP complexed form).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
302,
251-264)
copyright 2000.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Grinthal,
I.Adamovic,
B.Weiner,
M.Karplus,
and
N.Kleckner
(2010).
PR65, the HEAT-repeat scaffold of phosphatase PP2A, is an elastic connector that links force and catalysis.
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Proc Natl Acad Sci U S A,
107,
2467-2472.
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I.S.Seong,
J.M.Woda,
J.J.Song,
A.Lloret,
P.D.Abeyrathne,
C.J.Woo,
G.Gregory,
J.M.Lee,
V.C.Wheeler,
T.Walz,
R.E.Kingston,
J.F.Gusella,
R.A.Conlon,
and
M.E.Macdonald
(2010).
Huntingtin facilitates polycomb repressive complex 2.
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Hum Mol Genet,
19,
573-583.
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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.
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Structure,
18,
1171-1183.
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PDB code:
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C.Ptak,
A.M.Anderson,
R.J.Scott,
D.Van de Vosse,
R.S.Rogers,
Y.Sydorskyy,
J.D.Aitchison,
and
R.W.Wozniak
(2009).
A role for the karyopherin Kap123p in microtubule stability.
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Traffic,
10,
1619-1634.
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L.J.Terry,
and
S.R.Wente
(2009).
Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport.
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Eukaryot Cell,
8,
1814-1827.
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U.Zachariae,
and
H.Grubmüller
(2008).
Importin-beta: structural and dynamic determinants of a molecular spring.
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Structure,
16,
906-915.
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A.S.Madrid,
and
K.Weis
(2006).
Nuclear transport is becoming crystal clear.
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Chromosoma,
115,
98.
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H.Yagisawa
(2006).
Nucleocytoplasmic shuttling of phospholipase C-delta1: a link to Ca2+.
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J Cell Biochem,
97,
233-243.
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U.Zachariae,
and
H.Grubmüller
(2006).
A highly strained nuclear conformation of the exportin Cse1p revealed by molecular dynamics simulations.
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Structure,
14,
1469-1478.
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R.Nevo,
V.Brumfeld,
R.Kapon,
P.Hinterdorfer,
and
Z.Reich
(2005).
Direct measurement of protein energy landscape roughness.
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EMBO Rep,
6,
482-486.
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M.Koike,
S.Kose,
M.Furuta,
N.Taniguchi,
F.Yokoya,
Y.Yoneda,
and
N.Imamoto
(2004).
beta-Catenin shows an overlapping sequence requirement but distinct molecular interactions for its bidirectional passage through nuclear pores.
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J Biol Chem,
279,
34038-34047.
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M.Oeffinger,
M.Dlakic,
and
D.Tollervey
(2004).
A pre-ribosome-associated HEAT-repeat protein is required for export of both ribosomal subunits.
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Genes Dev,
18,
196-209.
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K.Weis
(2003).
Regulating access to the genome: nucleocytoplasmic transport throughout the cell cycle.
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Cell,
112,
441-451.
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R.Nevo,
C.Stroh,
F.Kienberger,
D.Kaftan,
V.Brumfeld,
M.Elbaum,
Z.Reich,
and
P.Hinterdorfer
(2003).
A molecular switch between alternative conformational states in the complex of Ran and importin beta1.
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Nat Struct Biol,
10,
553-557.
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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.
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Acta Crystallogr D Biol Crystallogr,
59,
1866-1868.
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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.
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Science,
302,
1571-1575.
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PDB code:
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T.Kumasaka,
M.Yamamoto,
E.Yamashita,
H.Moriyama,
and
T.Ueki
(2002).
Trichromatic concept optimizes MAD experiments in synchrotron X-ray crystallography.
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Structure,
10,
1205-1210.
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A.C.Ström,
and
K.Weis
(2001).
Importin-beta-like nuclear transport receptors.
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Genome Biol,
2,
REVIEWS3008.
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C.Steegborn,
O.Danot,
R.Huber,
and
T.Clausen
(2001).
Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization.
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Structure,
9,
1051-1060.
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PDB code:
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S.Prost,
S.Sheahan,
D.Rannie,
and
D.J.Harrison
(2001).
Adenovirus-mediated Cre deletion of floxed sequences in primary mouse cells is an efficient alternative for studies of gene deletion.
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Nucleic Acids Res,
29,
E80.
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N.Imamoto
(2000).
Diversity in nucleocytoplasmic transport pathways.
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Cell Struct Funct,
25,
207-216.
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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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Links
