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PDBsum entry 1sdf
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* Residue conservation analysis
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DOI no:
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Embo J
16:6996-7007
(1997)
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PubMed id:
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Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1.
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M.P.Crump,
J.H.Gong,
P.Loetscher,
K.Rajarathnam,
A.Amara,
F.Arenzana-Seisdedos,
J.L.Virelizier,
M.Baggiolini,
B.D.Sykes,
I.Clark-Lewis.
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ABSTRACT
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The three-dimensional structure of stromal cell-derived factor-1 (SDF-1) was
determined by NMR spectroscopy. SDF-1 is a monomer with a disordered N-terminal
region (residues 1-8), and differs from other chemokines in the packing of the
hydrophobic core and surface charge distribution. Results with analogs showed
that the N-terminal eight residues formed an important receptor binding site;
however, only Lys-1 and Pro-2 were directly involved in receptor activation.
Modification to Lys-1 and/or Pro-2 resulted in loss of activity, but generated
potent SDF-1 antagonists. Residues 12-17 of the loop region, which we term the
RFFESH motif, unlike the N-terminal region, were well defined in the SDF-1
structure. The RFFESH formed a receptor binding site, which we propose to be an
important initial docking site of SDF-1 with its receptor. The ability of the
SDF-1 analogs to block HIV-1 entry via CXCR4, which is a HIV-1 coreceptor for
the virus in addition to being the receptor for SDF-1, correlated with their
affinity for CXCR4. Activation of the receptor is not required for HIV-1
inhibition.
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Selected figure(s)
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Figure 1.
Figure 1 The structure of SDF-1. (A) A stereoview of a
superimposition of the 30 simulated annealing structures of
SDF-1 on the average structure. The RMS deviation for residues 9
-65 between all 30 structures and the average structure is 0.35
Å for backbone and 0.96 Å for heavy atoms. (B) A schematic
diagram showing the restrained minimized average structure of
SDF-1 created with the program MOLSCRIPT (Kraulis, 1991) and
Raster3D (Merritt and Murphy, 1994).
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Figure 7.
Figure 7 A model for interaction of SDF-1 with CXCR4. A
schematic depicting the interaction of SDF-1 with the receptor
is shown. CXCR4 is shown with the seven helices represented as
cylinders, which are connected by the surface and cytoplasmic
loops. The N-terminal and C-terminal segments of the receptor,
and the N- and C-terminus of SDF-1, are annotated as N and C.
SDF-1 is shown as a MOLSCRIPT diagram. (A) indicates the
receptor and ligand separately prior to any interaction between
the two. (B) indicates interaction of the SDF-1 RFFESH loop
(site 1) with the N-terminal segment of the receptor. The
contact region is shown in blue. Two of the helices are
truncated [compare with (A)] to highlight the binding groove of
the receptor. (C) Shows the N-terminal region (site 2) of SDF-1
bound in groove at the top of the helices (orange). Binding of
the N-terminal region results in activation of the receptor,
which is depicted in (C) by the change in conformation of the
receptor helices compared with (B).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
Embo J
(1997,
16,
6996-7007)
copyright 1997.
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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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Nature,
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PDB code:
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C.L.Salanga,
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PDB codes:
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J.W.Murphy,
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Proteins,
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PDB codes:
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K.Bellmann-Sickert,
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J Pept Sci,
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Protein Sci,
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PDB codes:
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H.Shim,
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and
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Structural basis of the interaction between chemokine stromal cell-derived factor-1/CXCL12 and its G-protein-coupled receptor CXCR4.
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Y.Tan,
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Biochemistry,
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C.T.Veldkamp,
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and
B.F.Volkman
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Structural basis of CXCR4 sulfotyrosine recognition by the chemokine SDF-1/CXCL12.
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Sci Signal,
1,
ra4.
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PDB codes:
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D.L.Theobald,
and
D.S.Wuttke
(2008).
Accurate structural correlations from maximum likelihood superpositions.
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PLoS Comput Biol,
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J.Meijer,
J.Ogink,
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Stem Cells,
26,
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An ectromelia virus protein that interacts with chemokines through their glycosaminoglycan binding domain.
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J Virol,
82,
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F.Rohmer,
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C.Franchet,
S.Lecat,
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Small neutralizing molecules to inhibit actions of the chemokine CXCL12.
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J Biol Chem,
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M.Thelen,
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Nat Immunol,
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Sulfated oligosaccharides (heparin and fucoidan) binding and dimerization of stromal cell-derived factor-1 (SDF-1/CXCL 12) are coupled as evidenced by affinity CE-MS analysis.
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Glycobiology,
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F.Arenzana-Seisdedos,
and
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PLoS ONE,
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C.T.Veldkamp,
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N.de la Cruz,
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Protein Expr Purif,
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D.Liu,
N.Madani,
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Crystal structure of recombinant human stromal cell-derived factor-1alpha.
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Proteins,
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PDB code:
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F.Asperti-Boursin,
E.Real,
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J Biol Chem,
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Structural and functional basis of CXCL12 (stromal cell-derived factor-1 alpha) binding to heparin.
|
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J Biol Chem,
282,
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PDB code:
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K.W.Christopherson,
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Stem Cells Dev,
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S.J.Allen,
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Annu Rev Immunol,
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T.Cardozo,
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H.Burger,
and
S.Zolla-Pazner
(2007).
Structural basis for coreceptor selectivity by the HIV type 1 V3 loop.
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AIDS Res Hum Retroviruses,
23,
415-426.
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W.Rostène,
P.Kitabgi,
and
S.M.Parsadaniantz
(2007).
Chemokines: a new class of neuromodulator?
|
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Nat Rev Neurosci,
8,
895-903.
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Y.Li,
D.Liu,
R.Cao,
S.Kumar,
C.Dong,
J.An,
S.R.Wilson,
Y.G.Gao,
and
Z.Huang
(2007).
Crystal structure of chemically synthesized vMIP-II.
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Proteins,
67,
243-246.
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PDB codes:
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C.T.Veldkamp,
C.Seibert,
F.C.Peterson,
T.P.Sakmar,
and
B.F.Volkman
(2006).
Recognition of a CXCR4 sulfotyrosine by the chemokine stromal cell-derived factor-1alpha (SDF-1alpha/CXCL12).
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J Mol Biol,
359,
1400-1409.
|
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D.K.Jin,
K.Shido,
H.G.Kopp,
I.Petit,
S.V.Shmelkov,
L.M.Young,
A.T.Hooper,
H.Amano,
S.T.Avecilla,
B.Heissig,
K.Hattori,
F.Zhang,
D.J.Hicklin,
Y.Wu,
Z.Zhu,
A.Dunn,
H.Salari,
Z.Werb,
N.R.Hackett,
R.G.Crystal,
D.Lyden,
and
S.Rafii
(2006).
Cytokine-mediated deployment of SDF-1 induces revascularization through recruitment of CXCR4+ hemangiocytes.
|
| |
Nat Med,
12,
557-567.
|
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G.Gaibelet,
T.Planchenault,
S.Mazères,
F.Dumas,
F.Arenzana-Seisdedos,
A.Lopez,
B.Lagane,
and
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| |
Protein Sci,
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PDB code:
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A.Coulomb-L'Hermin,
A.Amara,
C.Schiff,
I.Durand-Gasselin,
A.Foussat,
T.Delaunay,
G.Chaouat,
F.Capron,
N.Ledee,
P.Galanaud,
F.Arenzana-Seisdedos,
and
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(1999).
Stromal cell-derived factor 1 (SDF-1) and antenatal human B cell lymphopoiesis: expression of SDF-1 by mesothelial cells and biliary ductal plate epithelial cells.
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Proc Natl Acad Sci U S A,
96,
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B.J.Doranz,
M.J.Orsini,
J.D.Turner,
T.L.Hoffman,
J.F.Berson,
J.A.Hoxie,
S.C.Peiper,
L.F.Brass,
and
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Identification of CXCR4 domains that support coreceptor and chemokine receptor functions.
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J Virol,
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E.A.Berger,
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Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease.
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Annu Rev Immunol,
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M.P.Crump,
L.Spyracopoulos,
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Backbone dynamics of the human CC chemokine eotaxin: fast motions, slow motions, and implications for receptor binding.
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Protein Sci,
8,
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O.O.Yang,
S.L.Swanberg,
Z.Lu,
M.Dziejman,
J.McCoy,
A.D.Luster,
B.D.Walker,
and
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(1999).
Enhanced inhibition of human immunodeficiency virus type 1 by Met-stromal-derived factor 1beta correlates with down-modulation of CXCR4.
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J Virol,
73,
4582-4589.
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P.J.Klasse,
M.M.Rosenkilde,
N.Signoret,
A.Pelchen-Matthews,
T.W.Schwartz,
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CD4-Chemokine receptor hybrids in human immunodeficiency virus type 1 infection.
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J Virol,
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P.Proost,
S.Struyf,
D.Schols,
G.Opdenakker,
S.Sozzani,
P.Allavena,
A.Mantovani,
K.Augustyns,
G.Bal,
A.Haemers,
A.M.Lambeir,
S.Scharpé,
J.Van Damme,
and
I.De Meester
(1999).
Truncation of macrophage-derived chemokine by CD26/ dipeptidyl-peptidase IV beyond its predicted cleavage site affects chemotactic activity and CC chemokine receptor 4 interaction.
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J Biol Chem,
274,
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R.J.Nibbs,
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LD78beta, a non-allelic variant of human MIP-1alpha (LD78alpha), has enhanced receptor interactions and potent HIV suppressive activity.
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J Biol Chem,
274,
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V.Maréchal,
F.Arenzana-Seisdedos,
J.M.Heard,
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Opposite effects of SDF-1 on human immunodeficiency virus type 1 replication.
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J Virol,
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C.Dealwis,
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M.A.Siani,
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(1998).
Crystal structure of chemically synthesized [N33A] stromal cell-derived factor 1alpha, a potent ligand for the HIV-1 "fusin" coreceptor.
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Proc Natl Acad Sci U S A,
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PDB code:
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D.Missé,
M.Cerutti,
I.Schmidt,
A.Jansen,
G.Devauchelle,
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Dissociation of the CD4 and CXCR4 binding properties of human immunodeficiency virus type 1 gp120 by deletion of the first putative alpha-helical conserved structure.
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J Virol,
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J.S.Laurence,
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Effect of N-terminal truncation and solution conditions on chemokine dimer stability: nuclear magnetic resonance structural analysis of macrophage inflammatory protein 1 beta mutants.
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Biochemistry,
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J.Wilken,
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Chemical protein synthesis.
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M.P.Crump,
K.Rajarathnam,
K.S.Kim,
I.Clark-Lewis,
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(1998).
Solution structure of eotaxin, a chemokine that selectively recruits eosinophils in allergic inflammation.
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| |
J Biol Chem,
273,
22471-22479.
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PDB codes:
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|
|
N.Heveker,
M.Montes,
L.Germeroth,
A.Amara,
A.Trautmann,
M.Alizon,
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J.Schneider-Mergener
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Dissociation of the signalling and antiviral properties of SDF-1-derived small peptides.
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Curr Biol,
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N-terminal peptides of stromal cell-derived factor-1 with CXC chemokine receptor 4 agonist and antagonist activities.
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J Biol Chem,
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S.Sawada,
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Disturbed CD4+ T cell homeostasis and in vitro HIV-1 susceptibility in transgenic mice expressing T cell line-tropic HIV-1 receptors.
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J Exp Med,
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T.Shioda,
H.Kato,
Y.Ohnishi,
K.Tashiro,
M.Ikegawa,
E.E.Nakayama,
H.Hu,
A.Kato,
Y.Sakai,
H.Liu,
T.Honjo,
A.Nomoto,
A.Iwamoto,
C.Morimoto,
and
Y.Nagai
(1998).
Anti-HIV-1 and chemotactic activities of human stromal cell-derived factor 1alpha (SDF-1alpha) and SDF-1beta are abolished by CD26/dipeptidyl peptidase IV-mediated cleavage.
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Proc Natl Acad Sci U S A,
95,
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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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