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PDBsum entry 1nap
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* Residue conservation analysis
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J Biol Chem
270:7077-7087
(1995)
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PubMed id:
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The crystal structure of recombinant human neutrophil-activating peptide-2 (M6L) at 1.9-A resolution.
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M.G.Malkowski,
J.Y.Wu,
J.B.Lazar,
P.H.Johnson,
B.F.Edwards.
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ABSTRACT
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Neutrophil-activating peptide-2 (NAP-2) is a 70-residue carboxyl-terminal
fragment of platelet basic protein, which is found in the alpha-granules of
human platelets. NAP-2, which belongs to the CXC family of chemokines that
includes interleukin-8 and platelet factor 4, binds to the interleukin-8 type II
receptor and induces a rise in cytosolic calcium, chemotaxis of neutrophils, and
exocytosis. Crystals of recombinant NAP-2 in which the single methionine at
position 6 was replaced by leucine to facilitate expression belong to space
group P1 (unit cell parameters a = 40.8, b = 43.8, and c = 44.7 A and alpha =
98.4 degrees, beta = 120.3 degrees, and gamma = 92.8 degrees), with 4 molecules
of NAP-2 (Mr = 7600) in the asymmetric unit. The molecular replacement solution
calculated with bovine platelet factor 4 as the starting model was refined using
rigid body refinement, manual fitting in solvent-leveled electron density maps,
simulated annealing, and restrained least squares to an R-factor of 0.188 for 2
sigma data between 7.0- and 1.9-A resolution. The final refined crystal
structure includes 265 solvent molecules. The overall tertiary structure, which
is similar to that of platelet factor 4 and interleukin-8, includes an extended
amino-terminal loop, three strands of antiparallel beta-sheet arranged in a
Greek key fold, and one alpha-helix at the carboxyl terminus. The Glu-Leu-Arg
sequence that is critical for receptor binding is fully defined by electron
density and exhibits multiple conformations.
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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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Z.Cai,
C.Gao,
Y.Zhang,
and
K.Xing
(2009).
Functional characterization of the ELR motif in piscine ELR+CXC-like chemokine.
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Mar Biotechnol (NY),
11,
505-512.
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D.I.Chan,
H.N.Hunter,
B.F.Tack,
and
H.J.Vogel
(2008).
Human macrophage inflammatory protein 3alpha: protein and peptide nuclear magnetic resonance solution structures, dimerization, dynamics, and anti-infective properties.
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Antimicrob Agents Chemother,
52,
883-894.
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PDB code:
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T.Jabeen,
P.Leonard,
H.Jamaluddin,
and
K.R.Acharya
(2008).
Structure of mouse IP-10, a chemokine.
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Acta Crystallogr D Biol Crystallogr,
64,
611-619.
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PDB code:
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G.J.Swaminathan,
D.E.Holloway,
R.A.Colvin,
G.K.Campanella,
A.C.Papageorgiou,
A.D.Luster,
and
K.R.Acharya
(2003).
Crystal structures of oligomeric forms of the IP-10/CXCL10 chemokine.
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Structure,
11,
521-532.
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PDB codes:
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H.Lortat-Jacob,
A.Grosdidier,
and
A.Imberty
(2002).
Structural diversity of heparan sulfate binding domains in chemokines.
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Proc Natl Acad Sci U S A,
99,
1229-1234.
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X.L.Yang,
R.J.Skene,
D.E.McRee,
and
P.Schimmel
(2002).
Crystal structure of a human aminoacyl-tRNA synthetase cytokine.
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Proc Natl Acad Sci U S A,
99,
15369-15374.
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PDB code:
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Buyong,
J.Xiong,
J.Lubkowski,
and
R.Nussinov
(2000).
Homology modeling and molecular dynamics simulations of lymphotactin.
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Protein Sci,
9,
2192-2199.
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J.Blaszczyk,
E.V.Coillie,
P.Proost,
J.V.Damme,
G.Opdenakker,
G.D.Bujacz,
J.M.Wang,
and
X.Ji
(2000).
Complete crystal structure of monocyte chemotactic protein-2, a CC chemokine that interacts with multiple receptors.
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Biochemistry,
39,
14075-14081.
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PDB code:
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J.T.Ashfield,
T.Meyers,
D.Lowne,
P.G.Varley,
J.R.Arnold,
P.Tan,
J.C.Yang,
L.G.Czaplewski,
T.Dudgeon,
and
J.Fisher
(2000).
Chemical modification of a variant of human MIP-1alpha; implications for dimer structure.
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Protein Sci,
9,
2047-2053.
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H.Sticht,
S.E.Escher,
K.Schweimer,
W.G.Forssmann,
P.Rösch,
and
K.Adermann
(1999).
Solution structure of the human CC chemokine 2: A monomeric representative of the CC chemokine subtype.
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Biochemistry,
38,
5995-6002.
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PDB code:
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W.Shao,
L.F.Jerva,
J.West,
E.Lolis,
and
B.I.Schweitzer
(1998).
Solution structure of murine macrophage inflammatory protein-2.
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Biochemistry,
37,
8303-8313.
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PDB code:
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J.Lubkowski,
G.Bujacz,
L.Boqué,
P.J.Domaille,
T.M.Handel,
and
A.Wlodawer
(1997).
The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions.
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Nat Struct Biol,
4,
64-69.
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PDB codes:
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L.F.Jerva,
G.Sullivan,
and
E.Lolis
(1997).
Functional and receptor binding characterization of recombinant murine macrophage inflammatory protein 2: sequence analysis and mutagenesis identify receptor binding epitopes.
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Protein Sci,
6,
1643-1652.
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M.Baggiolini,
B.Dewald,
and
B.Moser
(1997).
Human chemokines: an update.
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Annu Rev Immunol,
15,
675-705.
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S.Meunier,
J.M.Bernassau,
J.C.Guillemot,
P.Ferrara,
and
H.Darbon
(1997).
Determination of the three-dimensional structure of CC chemokine monocyte chemoattractant protein 3 by 1H two-dimensional NMR spectroscopy.
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Biochemistry,
36,
4412-4422.
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PDB code:
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Y.Zhang,
and
B.J.Rollins
(1995).
A dominant negative inhibitor indicates that monocyte chemoattractant protein 1 functions as a dimer.
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Mol Cell Biol,
15,
4851-4855.
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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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