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415 a.a.
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46 a.a.
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220 a.a.
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214 a.a.
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* Residue conservation analysis
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PDB id:
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Protein transport/immune system
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Title:
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Crystal structure of secye translocon from thermus thermophilus with a fab fragment
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Structure:
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Preprotein translocase secy subunit. Chain: y. Fragment: residues 1-434. Engineered: yes. Mutation: yes. Preprotein translocase sece subunit. Chain: e. Engineered: yes. Fab56 (heavy chain).
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Source:
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Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. Mouse. Organism_taxid: 10090. Cell_line: hybridoma. Cell_line: hybridoma
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Resolution:
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3.20Å
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R-factor:
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0.246
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R-free:
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0.280
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Authors:
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T.Tsukazaki,H.Mori,S.Fukai,R.Ishitani,A.Perederina,D.G.Vassylyev, K.Ito,O.Nureki
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Key ref:
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T.Tsukazaki
et al.
(2008).
Conformational transition of Sec machinery inferred from bacterial SecYE structures.
Nature,
455,
988-991.
PubMed id:
DOI:
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Date:
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08-Mar-08
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Release date:
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14-Oct-08
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PROCHECK
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Headers
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References
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Q5SHQ8
(SECY_THET8) -
Protein translocase subunit SecY from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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Seq:
Struc:
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438 a.a.
415 a.a.*
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P38383
(SECE_THET8) -
Protein translocase subunit SecE from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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Seq:
Struc:
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60 a.a.
46 a.a.
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DOI no:
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Nature
455:988-991
(2008)
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PubMed id:
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Conformational transition of Sec machinery inferred from bacterial SecYE structures.
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T.Tsukazaki,
H.Mori,
S.Fukai,
R.Ishitani,
T.Mori,
N.Dohmae,
A.Perederina,
Y.Sugita,
D.G.Vassylyev,
K.Ito,
O.Nureki.
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ABSTRACT
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Over 30% of proteins are secreted across or integrated into membranes. Their
newly synthesized forms contain either cleavable signal sequences or
non-cleavable membrane anchor sequences, which direct them to the evolutionarily
conserved Sec translocon (SecYEG in prokaryotes and Sec61, comprising alpha-,
gamma- and beta-subunits, in eukaryotes). The translocon then functions as a
protein-conducting channel. These processes of protein localization occur either
at or after translation. In bacteria, the SecA ATPase drives post-translational
translocation. The only high-resolution structure of a translocon available so
far is that for SecYEbeta from the archaeon Methanococcus jannaschii, which
lacks SecA. Here we present the 3.2-A-resolution crystal structure of the SecYE
translocon from a SecA-containing organism, Thermus thermophilus. The structure,
solved as a complex with an anti-SecY Fab fragment, revealed a 'pre-open' state
of SecYE, in which several transmembrane helices are shifted, as compared to the
previous SecYEbeta structure, to create a hydrophobic crack open to the
cytoplasm. Fab and SecA bind to a common site at the tip of the cytoplasmic
domain of SecY. Molecular dynamics and disulphide mapping analyses suggest that
the pre-open state might represent a SecYE conformational transition that is
inducible by SecA binding. Moreover, we identified a SecA-SecYE interface that
comprises SecA residues originally buried inside the protein, indicating that
both the channel and the motor components of the Sec machinery undergo
cooperative conformational changes on formation of the functional complex.
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Selected figure(s)
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Figure 1.
Figure 1: Overall structure of T. thermophilus SecYE. a, b,
The SecYE complex viewed from the lateral gate side (a) and the
cytoplasm (b). The SecY transmembranes are coloured light blue
to red from the N to C termini, and SecE is coloured pink. Arg
351 (ref. 17) is coloured red and is shown in stick
representation. The residues coloured green in stick
representation were mutated to cysteine for intermolecular
crosslinking experiments.
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Figure 2.
Figure 2: Comparison of the T. thermophilus SecYE and M.
jannaschii SecYE beta- structures.
a, b, Molecular surfaces of SecYE (a) and SecYE  (b),
coloured as in Fig. 1a. Transmembrane regions are numbered. c,
d, The cytoplasmic regions of TM2, TM8 and TM9 of SecY. Pre-open
(c, crystal structure of Fab–SecYE) and closed forms (d,
without Fab, molecular dynamics analysis at 72.93 ns) are shown.
Numbers show distances between  carbons.
e, Intramolecular disulphide bond formation in SecY as assessed
by quantitative carboxymethylation. Averages of three analyses
are shown with s.d. f, SecA-mediated inhibition of SecY
(Thr92Cys–Val329Cys) intramolecular disulphide bond formation
in the presence of AMP-PNP.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
Nature
(2008,
455,
988-991)
copyright 2008.
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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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J.Frauenfeld,
J.Gumbart,
E.O.Sluis,
S.Funes,
M.Gartmann,
B.Beatrix,
T.Mielke,
O.Berninghausen,
T.Becker,
K.Schulten,
and
R.Beckmann
(2011).
Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
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Nat Struct Mol Biol,
18,
614-621.
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PDB codes:
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J.Gumbart,
C.Chipot,
and
K.Schulten
(2011).
Free-energy cost for translocon-assisted insertion of membrane proteins.
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Proc Natl Acad Sci U S A,
108,
3596-3601.
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M.Yamagishi,
H.Fujita,
F.Morimoto,
Y.Kida,
and
M.Sakaguchi
(2011).
A sugar chain at a specific position in the nascent polypeptide chain induces forward movement during translocation through the translocon.
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J Biochem,
149,
591-600.
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P.Kuhn,
B.Weiche,
L.Sturm,
E.Sommer,
F.Drepper,
B.Warscheid,
V.Sourjik,
and
H.G.Koch
(2011).
The bacterial SRP receptor, SecA and the ribosome use overlapping binding sites on the SecY translocon.
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Traffic,
12,
563-578.
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P.Palladino,
G.Saviano,
T.Tancredi,
E.Benedetti,
F.Rossi,
and
R.Ragone
(2011).
Structural determinants of protein translocation in bacteria: conformational flexibility of SecA IRA1 loop region.
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J Pept Sci,
17,
263-269.
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R.S.Hegde,
and
R.J.Keenan
(2011).
Tail-anchored membrane protein insertion into the endoplasmic reticulum.
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Nat Rev Mol Cell Biol,
12,
787-798.
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T.Tsukazaki,
H.Mori,
Y.Echizen,
R.Ishitani,
S.Fukai,
T.Tanaka,
A.Perederina,
D.G.Vassylyev,
T.Kohno,
A.D.Maturana,
K.Ito,
and
O.Nureki
(2011).
Structure and function of a membrane component SecDF that enhances protein export.
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Nature,
474,
235-238.
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PDB codes:
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A.N.Bondar,
C.del Val,
J.A.Freites,
D.J.Tobias,
and
S.H.White
(2010).
Dynamics of SecY translocons with translocation-defective mutations.
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Structure,
18,
847-857.
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A.Rychkova,
S.Vicatos,
and
A.Warshel
(2010).
On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes.
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Proc Natl Acad Sci U S A,
107,
17598-17603.
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B.Zhang,
and
T.F.Miller
(2010).
Hydrophobically stabilized open state for the lateral gate of the Sec translocon.
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Proc Natl Acad Sci U S A,
107,
5399-5404.
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H.Fujita,
Y.Kida,
M.Hagiwara,
F.Morimoto,
and
M.Sakaguchi
(2010).
Positive charges of translocating polypeptide chain retrieve an upstream marginal hydrophobic segment from the endoplasmic reticulum lumen to the translocon.
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Mol Biol Cell,
21,
2045-2056.
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I.C.Chen,
C.M.Yu,
Y.C.Lee,
Y.J.Huang,
H.J.Hsu,
and
A.S.Yang
(2010).
Signal sequence as a determinant in expressing disulfide-stabilized single chain antibody variable fragments (sc-dsFv) against human VEGF.
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Mol Biosyst,
6,
1307-1315.
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J.Tommassen
(2010).
Assembly of outer-membrane proteins in bacteria and mitochondria.
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Microbiology,
156,
2587-2596.
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K.Ito,
S.Chiba,
and
K.Pogliano
(2010).
Divergent stalling sequences sense and control cellular physiology.
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Biochem Biophys Res Commun,
393,
1-5.
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K.R.Vinothkumar,
and
R.Henderson
(2010).
Structures of membrane proteins.
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Q Rev Biophys,
43,
65.
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L.Anton,
K.Majander,
H.Savilahti,
L.Laakkonen,
and
B.Westerlund-Wikström
(2010).
Two distinct regions in the model protein Peb1 are critical for its heterologous transport out of Escherichia coli.
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Microb Cell Fact,
9,
97.
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P.F.Egea,
and
R.M.Stroud
(2010).
Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes.
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Proc Natl Acad Sci U S A,
107,
17182-17187.
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PDB code:
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R.Renthal
(2010).
Helix insertion into bilayers and the evolution of membrane proteins.
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Cell Mol Life Sci,
67,
1077-1088.
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S.J.Facey,
and
A.Kuhn
(2010).
Biogenesis of bacterial inner-membrane proteins.
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Cell Mol Life Sci,
67,
2343-2362.
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W.Chen,
Y.J.Huang,
S.R.Gundala,
H.Yang,
M.Li,
P.C.Tai,
and
B.Wang
(2010).
The first low microM SecA inhibitors.
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Bioorg Med Chem,
18,
1617-1625.
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Y.J.Huang,
I.C.Chen,
C.M.Yu,
Y.C.Lee,
H.J.Hsu,
A.T.Ching,
H.J.Chang,
and
A.S.Yang
(2010).
Engineering anti-vascular endothelial growth factor single chain disulfide-stabilized antibody variable fragments (sc-dsFv) with phage-displayed sc-dsFv libraries.
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J Biol Chem,
285,
7880-7891.
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Y.Kida,
C.Kume,
M.Hirano,
and
M.Sakaguchi
(2010).
Environmental transition of signal-anchor sequences during membrane insertion via the endoplasmic reticulum translocon.
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Mol Biol Cell,
21,
418-429.
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Z.Cheng
(2010).
Protein translocation through the Sec61/SecY channel.
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Biosci Rep,
30,
201-207.
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A.Y.Mulkidjanian,
and
M.Y.Galperin
(2009).
On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth.
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Biol Direct,
4,
27.
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B.C.Cross,
I.Sinning,
J.Luirink,
and
S.High
(2009).
Delivering proteins for export from the cytosol.
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Nat Rev Mol Cell Biol,
10,
255-264.
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B.W.Bauer,
and
T.A.Rapoport
(2009).
Mapping polypeptide interactions of the SecA ATPase during translocation.
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Proc Natl Acad Sci U S A,
106,
20800-20805.
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D.Boy,
and
H.G.Koch
(2009).
Visualization of distinct entities of the SecYEG translocon during translocation and integration of bacterial proteins.
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Mol Biol Cell,
20,
1804-1815.
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D.J.du Plessis,
G.Berrelkamp,
N.Nouwen,
and
A.J.Driessen
(2009).
The lateral gate of SecYEG opens during protein translocation.
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J Biol Chem,
284,
15805-15814.
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E.C.Mandon,
S.F.Trueman,
and
R.Gilmore
(2009).
Translocation of proteins through the Sec61 and SecYEG channels.
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Curr Opin Cell Biol,
21,
501-507.
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J.Gumbart,
L.G.Trabuco,
E.Schreiner,
E.Villa,
and
K.Schulten
(2009).
Regulation of the protein-conducting channel by a bound ribosome.
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Structure,
17,
1453-1464.
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PDB codes:
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K.Inaba,
S.Murakami,
A.Nakagawa,
H.Iida,
M.Kinjo,
K.Ito,
and
M.Suzuki
(2009).
Dynamic nature of disulphide bond formation catalysts revealed by crystal structures of DsbB.
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EMBO J,
28,
779-791.
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PDB codes:
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T.Becker,
S.Bhushan,
A.Jarasch,
J.P.Armache,
S.Funes,
F.Jossinet,
J.Gumbart,
T.Mielke,
O.Berninghausen,
K.Schulten,
E.Westhof,
R.Gilmore,
E.C.Mandon,
and
R.Beckmann
(2009).
Structure of monomeric yeast and Mammalian sec61 complexes interacting with the translating ribosome.
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Science,
326,
1369-1373.
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PDB codes:
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X.Zhao,
and
J.Jäntti
(2009).
Functional characterization of the trans-membrane domain interactions of the Sec61 protein translocation complex beta-subunit.
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BMC Cell Biol,
10,
76.
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A.Economou
(2008).
Structural biology: Clamour for a kiss.
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Nature,
455,
879-880.
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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
codes are
shown on the right.
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Links
