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PDBsum entry 1klo
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* Residue conservation analysis
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DOI no:
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J Mol Biol
257:644-657
(1996)
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PubMed id:
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Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site.
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J.Stetefeld,
U.Mayer,
R.Timpl,
R.Huber.
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ABSTRACT
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The structure of three consecutive laminin-type EGF-like (LE) modules of mouse
laminin gammma1 chain, gamma1III3-5 (positions 738 to 899), has been determined
by multiple isomorphous replacement in a crystal of space group p6(4)22
(a=b=74.57 angstroms, c = 185.11 angstroms and gamma = 120 degrees). The crystal
structure was refined using restrained crystallographic refinement to an
R-factor of 19.72% for 14,983 independent reflections with intensities
F(obs)> 0 at 2.1 angstroms resolution, with root mean square deviation of
0.012 angstroms and 1.690 degrees from ideal bond lengths and bond angles,
respectively. The final model consisted of 1179 (non-hydrogen) protein atoms
within 162 residues and 119 water molecules. The molecule showed a rod-like
structure of about 76 angstroms length with individual modules twisted relative
to each other by about 70 degrees. Each module has the same disulfide bond
connections Cys1-Cys3 (loop a), Cys2-Cys4 (loop b), Cys5-Cys6 (loop c) and
Cys7-Cys8 (loop d), the first three being identical to epidermal growth factor
(EGF). All three LE modules showed little secondary structure which was mainly
restricted to loop d, but they differed in several other details of their
structure. The interface contacts between the LE modules are based on hydrogen
bonds and hydrophobic interactions between the hydrophobic core of loop d of the
preceding module and the first cysteine and an exposed residue in loop b of the
following module. Module 4 was previously shown to contribute the major nidogen
binding site of laminis and site-directed mutagenesis demonstrated a specific
binding role for Asp800, Asn802, Val804 and Tyr819 in loops a and c. The
side-chain of these four residues are all located on the surface in a linear
array and separated by a distance of 17 angstroms between Tyr819 and Val804. The
entire nidogen binding site is stabilized via main-chain hydrogen bonds which
are in part derived from the link between loops b and c (residues Leu815 and
Lys816). The data demonstrate the unique nature of the LE modules and only a
remote similarity to EGF. They also indicate that the crucial residues in the
binding loops provide direct contacts with nidogen and explain the synergism
between loops a and c which is essential for binding.
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Selected figure(s)
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Figure 1.
Figure 1. View of the overall topology of the g1III3-5 module, emphasizing the secondary structural elements.
b-Strands are drawn as arrows and helical segments as spirals. Sequence positions of disulfide bridges are identified
and shown in yellow. Module 3 is in red, module 4 in grey, and module 5 in green. All drawings of the structure were
made with the program MOLSCRIPT (Kraulius, 1991).
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Figure 6.
Figure 6. Structural comparison of the EGF1 module of factor IXa (top) and LE module g1III4 (bottom) emphasizing
the different arrangement and sizes of the disulfide loops a to c and a to d. Disulfide bridges are shown in yellow. C,
C terminus; N, N terminus. The data for EGF1 were from Brandstetter et al. (1995).
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
257,
644-657)
copyright 1996.
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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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EMBO Rep,
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PDB code:
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PDB code:
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J Biol Chem,
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Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.
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Proteins,
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Evolution of distinct EGF domains with specific functions.
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Protein Sci,
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A nonsense mutation in the Arg345 of the insulin receptor gene in a Japanese type A insulin-resistant patient.
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Endocr J,
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M.Zacharias
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ATTRACT: protein-protein docking in CAPRI using a reduced protein model.
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Proteins,
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N.Gersdorff,
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T.Sasaki,
R.Timpl,
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Laminin gamma3 chain binds to nidogen and is located in murine basement membranes.
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J Biol Chem,
280,
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P.Carter,
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Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI.
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Proteins,
60,
281-288.
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S.Vajda
(2005).
Classification of protein complexes based on docking difficulty.
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Proteins,
60,
176-180.
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X.H.Ma,
C.H.Li,
L.Z.Shen,
X.Q.Gong,
W.Z.Chen,
and
C.X.Wang
(2005).
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition.
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Proteins,
60,
319-323.
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Y.Inbar,
D.Schneidman-Duhovny,
I.Halperin,
A.Oron,
R.Nussinov,
and
H.J.Wolfson
(2005).
Approaching the CAPRI challenge with an efficient geometry-based docking.
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Proteins,
60,
217-223.
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S.J.Wodak,
and
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Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications.
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Curr Opin Struct Biol,
14,
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J.T.Dessens,
I.Sidén-Kiamos,
J.Mendoza,
V.Mahairaki,
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(2003).
SOAP, a novel malaria ookinete protein involved in mosquito midgut invasion and oocyst development.
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Mol Microbiol,
49,
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J.Takagi,
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J.H.Liu,
J.H.Wang,
and
T.A.Springer
(2003).
Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface.
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Nature,
424,
969-974.
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PDB code:
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S.Schenk,
and
V.Quaranta
(2003).
Tales from the crypt[ic] sites of the extracellular matrix.
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Trends Cell Biol,
13,
366-375.
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J.L.Bodmer,
P.Schneider,
and
J.Tschopp
(2002).
The molecular architecture of the TNF superfamily.
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Trends Biochem Sci,
27,
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M.Doi,
J.Thyboll,
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R.Timpl,
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and
K.Tryggvason
(2002).
Recombinant human laminin-10 (alpha5beta1gamma1). Production, purification, and migration-promoting activity on vascular endothelial cells.
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J Biol Chem,
277,
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T.Sasaki,
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N.Miosge,
and
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(2002).
Domain IV of mouse laminin beta1 and beta2 chains.
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Eur J Biochem,
269,
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C.W.Ward,
T.P.Garrett,
N.M.McKern,
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L.J.Cosgrove,
L.G.Sparrow,
M.J.Frenkel,
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L.J.Lawrence,
and
P.A.Tulloch
(2001).
The three dimensional structure of the type I insulin-like growth factor receptor.
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Mol Pathol,
54,
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S.R.Campion,
A.S.Ameen,
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J.M.King,
and
T.N.Munzenmaier
(2001).
Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.
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Proteins,
44,
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P.Tunggal,
N.Smyth,
M.Paulsson,
and
M.C.Ott
(2000).
Laminins: structure and genetic regulation.
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Microsc Res Tech,
51,
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and
A.W.Burgess
(2000).
Characterization of a comparative model of the extracellular domain of the epidermal growth factor receptor.
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Protein Sci,
9,
310-324.
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PDB codes:
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S.R.Hubbard,
and
J.H.Till
(2000).
Protein tyrosine kinase structure and function.
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Annu Rev Biochem,
69,
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A.Iivanainen,
T.Morita,
and
K.Tryggvason
(1999).
Molecular cloning and tissue-specific expression of a novel murine laminin gamma3 chain.
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J Biol Chem,
274,
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B.M.Veneziani,
F.Giallauria,
and
F.Gentile
(1999).
The disulfide bond pattern between fragments obtained by the limited proteolysis of bovine thyroglobulin.
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Biochimie,
81,
517-525.
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M.Hopf,
W.Göhring,
E.Kohfeldt,
Y.Yamada,
and
R.Timpl
(1999).
Recombinant domain IV of perlecan binds to nidogens, laminin-nidogen complex, fibronectin, fibulin-2 and heparin.
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Eur J Biochem,
259,
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A.J.Denzer,
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and
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Electron microscopic structure of agrin and mapping of its binding site in laminin-1.
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EMBO J,
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U.Mayer,
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(1998).
Structural and genetic analysis of laminin-nidogen interaction.
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Ann N Y Acad Sci,
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J Biol Chem,
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Eur J Biochem,
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Analysis of 4-1BBL and laminin binding to murine 4-1BB, a member of the tumor necrosis factor receptor superfamily, and comparison with human 4-1BB.
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Macromolecular organization of basement membranes.
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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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