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* Residue conservation analysis
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PDB id:
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Protein transport
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Title:
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Crystal structure of human importin beta bound to the snurportin1 ibb- domain second crystal form
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Structure:
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Importin beta-1 subunit. Chain: a, b. Synonym: karyopherin beta-1 subunit, nuclear factor p97, importin 90. Engineered: yes. Snurportin-1. Chain: c, d. Fragment: n-terminal domain (25-64). Synonym: RNA u transporter 1. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: kpnb1, ntf97. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Organism_taxid: 9606
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Resolution:
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3.20Å
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R-factor:
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0.303
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R-free:
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0.328
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Authors:
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G.Mitrousis,G.Cingolani
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Key ref:
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G.Mitrousis
et al.
(2008).
Molecular basis for the recognition of snurportin 1 by importin beta.
J Biol Chem,
283,
7877-7884.
PubMed id:
DOI:
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Date:
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31-May-07
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Release date:
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22-Jan-08
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PROCHECK
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Headers
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References
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Q14974
(IMB1_HUMAN) -
Importin subunit beta-1 from Homo sapiens
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Seq:
Struc:
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876 a.a.
871 a.a.
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DOI no:
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J Biol Chem
283:7877-7884
(2008)
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PubMed id:
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Molecular basis for the recognition of snurportin 1 by importin beta.
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G.Mitrousis,
A.S.Olia,
N.Walker-Kopp,
G.Cingolani.
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ABSTRACT
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The nuclear import of uridine-rich ribonucleoproteins is mediated by the
transport adaptor snurportin 1 (SNP1). Similar to importin alpha, SNP1 uses an
N-terminal importin beta binding (sIBB) domain to recruit the receptor importin
beta and gain access to the nucleus. In this study, we demonstrate that the sIBB
domain has a bipartite nature, which contains two distinct binding determinants
for importin beta. The first determinant spans residues 25-65 and includes the
previously identified importin alpha IBB (alphaIBB) region of homology. The
second binding determinant encompasses residues 1-24 and resembles region
1011-1035 of the nucleoporin 153 (Nup153). The two binding determinants
synergize within the sIBB domain to confer a low nanomolar binding affinity for
importin beta (K(d) approximately 2 nm) in an interaction that, in vitro, is
displaced by RanGTP. We propose that in vivo the synergy of Nup153 and nuclear
RanGTP promotes translocation of uridine-rich ribonucleoproteins into the
nucleus.
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Selected figure(s)
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Figure 2.
FIGURE 2. Structural plasticity of importin β bound to the
sIBB-(25-65) domain. a, ribbon diagram of the asymmetric unit
content of crystal form II, determined at 3.2 Å
resolution. The two complexes in the asymmetric unit have
different conformations. In complex B, on the left (in cyan),
importin β adopts an open conformation, and only the
sIBB-(40-65) helix is visible (in yellow). In complex A, on the
right (in green), importin β has a conformation identical to
crystal form I, and all residues for the sIBB-(25-65) domain are
visible (in magenta). b, superimposition of the importin β
structures from complex A (closed) and B (open) reveals
deviations up to 20 Å in the C terminus of the protein.
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Figure 3.
FIGURE 3. sIBB-(25-65) domain versus  IBB-(11-54) domain. a,
left panel, structure of importin β- IBB complex (in purple
and blue, respectively) superimposed to that of the importin
β-sIBB-(25-65) complex (in green and magenta, respectively) of
crystal form I. Right panel, blowup of the IBB and sIBB-(25-65)
domains (colored in blue and magenta, respectively) translated
out of the superimposition. Significant differences are observed
in the structure of the two peptides. b, schematic diagram of
the interactions between HEAT repeats 7-19 of importin β and
the sIBB-(25-65) domain (top) as compared with the IBB-(11-54) domain
(bottom). HEAT repeats are referred to as H7-19. Colored in red
in the primary sequence of the sIBB-(25-65) and IBB-(11-54) domain are
identical residues. Intermolecular polar and hydrophobic
interactions are shown as red and green lines, respectively.
Intramolecular contacts within IBB domains are indicated by red
brackets.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2008,
283,
7877-7884)
copyright 2008.
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Figures were
selected
by the author.
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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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M.Grünwald,
and
F.Bono
(2011).
Structure of Importin13-Ubc9 complex: nuclear import and release of a key regulator of sumoylation.
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EMBO J,
30,
427-438.
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PDB code:
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A.R.Lowe,
J.J.Siegel,
P.Kalab,
M.Siu,
K.Weis,
and
J.T.Liphardt
(2010).
Selectivity mechanism of the nuclear pore complex characterized by single cargo tracking.
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Nature,
467,
600-603.
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E.Kühn-Hölsken,
C.Lenz,
A.Dickmanns,
H.H.Hsiao,
F.M.Richter,
B.Kastner,
R.Ficner,
and
H.Urlaub
(2010).
Mapping the binding site of snurportin 1 on native U1 snRNP by cross-linking and mass spectrometry.
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Nucleic Acids Res,
38,
5581-5593.
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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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R.L.Rich,
and
D.G.Myszka
(2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
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J Mol Recognit,
23,
1.
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E.W.Debler,
G.Blobel,
and
A.Hoelz
(2009).
Nuclear transport comes full circle.
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Nat Struct Mol Biol,
16,
457-459.
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K.E.Lundin,
O.E.Simonson,
P.M.Moreno,
E.M.Zaghloul,
I.I.Oprea,
M.G.Svahn,
and
C.I.Smith
(2009).
Nanotechnology approaches for gene transfer.
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Genetica,
137,
47-56.
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N.Freitas,
and
C.Cunha
(2009).
Mechanisms and signals for the nuclear import of proteins.
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Curr Genomics,
10,
550-557.
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P.M.Moreno,
M.Wenska,
K.E.Lundin,
O.Wrange,
R.Strömberg,
and
C.I.Smith
(2009).
A synthetic snRNA m3G-CAP enhances nuclear delivery of exogenous proteins and nucleic acids.
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Nucleic Acids Res,
37,
1925-1935.
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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.
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Science,
324,
1087-1091.
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PDB code:
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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.
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Nature,
458,
1136-1141.
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PDB codes:
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X.Dong,
A.Biswas,
and
Y.M.Chook
(2009).
Structural basis for assembly and disassembly of the CRM1 nuclear export complex.
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Nat Struct Mol Biol,
16,
558-560.
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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
