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PDBsum entry 1k9i
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Sugar binding protein
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PDB id
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1k9i
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Contents |
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* Residue conservation analysis
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PDB id:
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Sugar binding protein
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Title:
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Complex of dc-sign and glcnac2man3
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Structure:
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Mdc-sign1b type i isoform. Chain: a, b, c, d, e, f, g, h, i, j. Fragment: carbohydrate recognition domain. Synonym: dc-sign receptor (dendritic cell-specific icam-3 grabbing nonintegrin). Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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15mer (from
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Resolution:
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2.50Å
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R-factor:
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0.213
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R-free:
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0.258
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Authors:
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H.Feinberg,D.A.Mitchell,K.Drickamer,W.I.Weis
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Key ref:
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H.Feinberg
et al.
(2001).
Structural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR.
Science,
294,
2163-2166.
PubMed id:
DOI:
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Date:
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29-Oct-01
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Release date:
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21-Dec-01
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PROCHECK
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Headers
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References
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Q9NNX6
(CD209_HUMAN) -
CD209 antigen from Homo sapiens
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Seq:
Struc:
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404 a.a.
128 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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DOI no:
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Science
294:2163-2166
(2001)
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PubMed id:
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Structural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR.
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H.Feinberg,
D.A.Mitchell,
K.Drickamer,
W.I.Weis.
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ABSTRACT
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Dendritic cell specific intracellular adhesion molecule-3 (ICAM-3) grabbing
nonintegrin (DC-SIGN), a C-type lectin present on the surface of dendritic
cells, mediates the initial interaction of dendritic cells with T cells by
binding to ICAM-3. DC-SIGN and DC-SIGNR, a related receptor found on the
endothelium of liver sinusoids, placental capillaries, and lymph nodes, bind to
oligosaccharides that are present on the envelope of human immunodeficiency
virus (HIV), an interaction that strongly promotes viral infection of T cells.
Crystal structures of carbohydrate-recognition domains of DC-SIGN and of
DC-SIGNR bound to oligosaccharide, in combination with binding studies, reveal
that these receptors selectively recognize endogenous high-mannose
oligosaccharides and may represent a new avenue for developing HIV prophylactics.
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Selected figure(s)
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Figure 1.
Fig. 1. Oligosaccharide structures. (A) The pentasaccharide
co-crystallized with both DC-SIGN and DC-SIGNR. Residue numbers
used in the text are shown in parentheses. (B) N-linked
high-mannose structure. The full nine-mannose structure (Man[9])
is shown, but the presence of  1-2 linked
mannose at the branch termini is variable. The inner branched
trimannose structure Man 1-3 [Man
1-6]Man is
shown in the red box, and the outer trimannose structure is
shown in the yellow box. (C) Typical N-linked complex
carbohydrate. The portion equivalent to the pentasaccharide used
in this study is boxed in red. The inner trimannose structure is
common to both complex and high-mannose N-linked
oligosaccharides. Gal, galactose; GlcNAc, N-acetylglucosamine;
Man, mannose; Sia, sialic acid.
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Figure 4.
Fig. 4. A phenylalanine prevents binding of the inner
trimannosyl core of N-linked oligosaccharides. The DC-SIGNR CRD
is shown in cyan, with the Phe^325 side chain in a
ball-and-stick representation. In yellow-green, the outer
branched trimannose structure of Man[9] was superimposed on the
trimannose structure seen in the DC-SIGNR crystals. For clarity,
only the 1-6 branch
is shown. In magenta, the mannose residue of a model of the
internal Man  1-4GlcNAc
1-4GlcNAc
moiety of N-linked oligosaccharides was superimposed on the
central (reducing) mannose of the trimannose structure. The
model was made by setting the torsion angles of the glycosidic
linkages to their average values found in an oligosaccharide
structure database (13), with adjustments in the torsion angles
to overlay the branched trimannose structure precisely. The
clash of the first GlcNAc with Phe^325 is evident. In both the
positions of the 1-3 and
1-6 linked
mannose residues linked to the central mannose of the trimannose
structure are indicated in the black text.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2001,
294,
2163-2166)
copyright 2001.
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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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A.Tai,
S.Froelich,
K.I.Joo,
and
P.Wang
(2011).
Production of lentiviral vectors with enhanced efficiency to target dendritic cells by attenuating mannosidase activity of mammalian cells.
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J Biol Eng,
5,
1.
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R.Ilyas,
R.Wallis,
E.J.Soilleux,
P.Townsend,
D.Zehnder,
B.K.Tan,
R.B.Sim,
H.Lehnert,
H.S.Randeva,
and
D.A.Mitchell
(2011).
High glucose disrupts oligosaccharide recognition function via competitive inhibition: a potential mechanism for immune dysregulation in diabetes mellitus.
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Immunobiology,
216,
126-131.
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S.J.Dilly,
A.J.Clark,
D.A.Mitchell,
A.Marsh,
and
P.C.Taylor
(2011).
Using the Man(9)(GlcNAc)(2)-DC-SIGN pairing to probe specificity in photochemical immobilization.
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Mol Biosyst,
7,
116-118.
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A.D.Regan,
D.G.Ousterout,
and
G.R.Whittaker
(2010).
Feline lectin activity is critical for the cellular entry of feline infectious peritonitis virus.
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J Virol,
84,
7917-7921.
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A.E.Zeituni,
W.McCaig,
E.Scisci,
D.G.Thanassi,
and
C.W.Cutler
(2010).
The native 67-kilodalton minor fimbria of Porphyromonas gingivalis is a novel glycoprotein with DC-SIGN-targeting motifs.
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J Bacteriol,
192,
4103-4110.
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A.L.Webber,
B.Elena,
J.M.Griffin,
J.R.Yates,
T.N.Pham,
F.Mauri,
C.J.Pickard,
A.M.Gil,
R.Stein,
A.Lesage,
L.Emsley,
and
S.P.Brown
(2010).
Complete (1)H resonance assignment of beta-maltose from (1)H-(1)H DQ-SQ CRAMPS and (1)H (DQ-DUMBO)-(13)C SQ refocused INEPT 2D solid-state NMR spectra and first principles GIPAW calculations.
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Phys Chem Chem Phys,
12,
6970-6983.
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C.Chaipan,
I.Steffen,
T.S.Tsegaye,
S.Bertram,
I.Glowacka,
Y.Kato,
J.Schmökel,
J.Münch,
G.Simmons,
R.Gerardy-Schahn,
and
S.Pöhlmann
(2010).
Incorporation of podoplanin into HIV released from HEK-293T cells, but not PBMC, is required for efficient binding to the attachment factor CLEC-2.
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Retrovirology,
7,
47.
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C.Flaujac,
S.Boukour,
and
E.Cramer-Bordé
(2010).
Platelets and viruses: an ambivalent relationship.
|
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Cell Mol Life Sci,
67,
545-556.
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H.Feinberg,
A.S.Powlesland,
M.E.Taylor,
and
W.I.Weis
(2010).
Trimeric structure of langerin.
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J Biol Chem,
285,
13285-13293.
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PDB code:
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H.L.Birch,
L.J.Alderwick,
B.J.Appelmelk,
J.Maaskant,
A.Bhatt,
A.Singh,
J.Nigou,
L.Eggeling,
J.Geurtsen,
and
G.S.Besra
(2010).
A truncated lipoglycan from mycobacteria with altered immunological properties.
|
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Proc Natl Acad Sci U S A,
107,
2634-2639.
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K.Matsuno,
N.Kishida,
K.Usami,
M.Igarashi,
R.Yoshida,
E.Nakayama,
M.Shimojima,
H.Feldmann,
T.Irimura,
Y.Kawaoka,
and
A.Takada
(2010).
Different potential of C-type lectin-mediated entry between Marburg virus strains.
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J Virol,
84,
5140-5147.
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K.Morizono,
A.Ku,
Y.Xie,
A.Harui,
S.K.Kung,
M.D.Roth,
B.Lee,
and
I.S.Chen
(2010).
Redirecting lentiviral vectors pseudotyped with sindbis virus-derived envelope proteins to DC-SIGN by modification of N-linked glycans of envelope proteins.
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J Virol,
84,
6923-6934.
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M.Kielian,
C.Chanel-Vos,
and
M.Liao
(2010).
Alphavirus Entry and Membrane Fusion.
|
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Viruses,
2,
796-825.
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M.V.Carroll,
R.B.Sim,
F.Bigi,
A.Jäkel,
R.Antrobus,
and
D.A.Mitchell
(2010).
Identification of four novel DC-SIGN ligands on Mycobacterium bovis BCG.
|
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Protein Cell,
1,
859-870.
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N.P.Chung,
S.K.Breun,
A.Bashirova,
J.G.Baumann,
T.D.Martin,
J.M.Karamchandani,
J.W.Rausch,
S.F.Le Grice,
L.Wu,
M.Carrington,
and
V.N.Kewalramani
(2010).
HIV-1 transmission by dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN) is regulated by determinants in the carbohydrate recognition domain that are absent in liver/lymph node-SIGN (L-SIGN).
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J Biol Chem,
285,
2100-2112.
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N.Shibata,
and
Y.Okawa
(2010).
Enzymatic synthesis of new oligosaccharides using mannosyltransferases from Candida species and their NMR assignments.
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Biol Pharm Bull,
33,
895-899.
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P.J.Coombs,
R.Harrison,
S.Pemberton,
A.Quintero-Martinez,
S.Parry,
S.M.Haslam,
A.Dell,
M.E.Taylor,
and
K.Drickamer
(2010).
Identification of novel contributions to high-affinity glycoprotein-receptor interactions using engineered ligands.
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J Mol Biol,
396,
685-696.
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R.Yabe,
H.Tateno,
and
J.Hirabayashi
(2010).
Frontal affinity chromatography analysis of constructs of DC-SIGN, DC-SIGNR and LSECtin extend evidence for affinity to agalactosylated N-glycans.
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FEBS J,
277,
4010-4026.
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V.Coelho,
S.Krysov,
A.M.Ghaemmaghami,
M.Emara,
K.N.Potter,
P.Johnson,
G.Packham,
L.Martinez-Pomares,
and
F.K.Stevenson
(2010).
Glycosylation of surface Ig creates a functional bridge between human follicular lymphoma and microenvironmental lectins.
|
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Proc Natl Acad Sci U S A,
107,
18587-18592.
|
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|
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Y.Zhou,
K.Lu,
S.Pfefferle,
S.Bertram,
I.Glowacka,
C.Drosten,
S.Pöhlmann,
and
G.Simmons
(2010).
A single asparagine-linked glycosylation site of the severe acute respiratory syndrome coronavirus spike glycoprotein facilitates inhibition by mannose-binding lectin through multiple mechanisms.
|
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J Virol,
84,
8753-8764.
|
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|
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A.E.Zeituni,
R.Jotwani,
J.Carrion,
and
C.W.Cutler
(2009).
Targeting of DC-SIGN on human dendritic cells by minor fimbriated Porphyromonas gingivalis strains elicits a distinct effector T cell response.
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J Immunol,
183,
5694-5704.
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A.Pashov,
S.Garimalla,
B.Monzavi-Karbassi,
and
T.Kieber-Emmons
(2009).
Carbohydrate targets in HIV vaccine research: lessons from failures.
|
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Immunotherapy,
1,
777-794.
|
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|
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B.Ernst,
and
J.L.Magnani
(2009).
From carbohydrate leads to glycomimetic drugs.
|
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Nat Rev Drug Discov,
8,
661-677.
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E.P.Go,
Q.Chang,
H.X.Liao,
L.L.Sutherland,
S.M.Alam,
B.F.Haynes,
and
H.Desaire
(2009).
Glycosylation site-specific analysis of clade C HIV-1 envelope proteins.
|
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J Proteome Res,
8,
4231-4242.
|
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G.Tabarani,
M.Thépaut,
D.Stroebel,
C.Ebel,
C.Vivès,
P.Vachette,
D.Durand,
and
F.Fieschi
(2009).
DC-SIGN neck domain is a pH-sensor controlling oligomerization: SAXS and hydrodynamic studies of extracellular domain.
|
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J Biol Chem,
284,
21229-21240.
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|
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J.Vidal-Dupiol,
M.Adjeroud,
E.Roger,
L.Foure,
D.Duval,
Y.Mone,
C.Ferrier-Pages,
E.Tambutte,
S.Tambutte,
D.Zoccola,
D.Allemand,
and
G.Mitta
(2009).
Coral bleaching under thermal stress: putative involvement of host/symbiont recognition mechanisms.
|
| |
BMC Physiol,
9,
14.
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K.Hacker,
L.White,
and
A.M.de Silva
(2009).
N-Linked glycans on dengue viruses grown in mammalian and insect cells.
|
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J Gen Virol,
90,
2097-2106.
|
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|
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|
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M.E.Taylor,
and
K.Drickamer
(2009).
Structural insights into what glycan arrays tell us about how glycan-binding proteins interact with their ligands.
|
| |
Glycobiology,
19,
1155-1162.
|
|
|
|
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|
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O.Martínez-Avila,
K.Hijazi,
M.Marradi,
C.Clavel,
C.Campion,
C.Kelly,
and
S.Penadés
(2009).
Gold manno-glyconanoparticles: multivalent systems to block HIV-1 gp120 binding to the lectin DC-SIGN.
|
| |
Chemistry,
15,
9874-9888.
|
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|
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O.Martínez-Avila,
L.M.Bedoya,
M.Marradi,
C.Clavel,
J.Alcamí,
and
S.Penadés
(2009).
Multivalent manno-glyconanoparticles inhibit DC-SIGN-mediated HIV-1 trans-infection of human T cells.
|
| |
Chembiochem,
10,
1806-1809.
|
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|
|
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|
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R.D.Cummings
(2009).
The repertoire of glycan determinants in the human glycome.
|
| |
Mol Biosyst,
5,
1087-1104.
|
|
|
|
|
|
|
S.A.Graham,
S.A.Jégouzo,
S.Yan,
A.S.Powlesland,
J.P.Brady,
M.E.Taylor,
and
K.Drickamer
(2009).
Prolectin, a Glycan-binding Receptor on Dividing B Cells in Germinal Centers.
|
| |
J Biol Chem,
284,
18537-18544.
|
|
|
|
|
|
|
S.I.Gringhuis,
J.den Dunnen,
M.Litjens,
M.van der Vlist,
and
T.B.Geijtenbeek
(2009).
Carbohydrate-specific signaling through the DC-SIGN signalosome tailors immunity to Mycobacterium tuberculosis, HIV-1 and Helicobacter pylori.
|
| |
Nat Immunol,
10,
1081-1088.
|
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|
|
|
|
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S.J.Park,
and
B.Mehrad
(2009).
Innate immunity to Aspergillus species.
|
| |
Clin Microbiol Rev,
22,
535-551.
|
|
|
|
|
|
|
S.Menon,
K.Rosenberg,
S.A.Graham,
E.M.Ward,
M.E.Taylor,
K.Drickamer,
and
D.E.Leckband
(2009).
Binding-site geometry and flexibility in DC-SIGN demonstrated with surface force measurements.
|
| |
Proc Natl Acad Sci U S A,
106,
11524-11529.
|
|
|
|
|
|
|
A.Bugarcic,
K.Hitchens,
A.G.Beckhouse,
C.A.Wells,
R.B.Ashman,
and
H.Blanchard
(2008).
Human and mouse macrophage-inducible C-type lectin (Mincle) bind Candida albicans.
|
| |
Glycobiology,
18,
679-685.
|
|
|
|
|
|
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A.Cambi,
M.G.Netea,
H.M.Mora-Montes,
N.A.Gow,
S.V.Hato,
D.W.Lowman,
B.J.Kullberg,
R.Torensma,
D.L.Williams,
and
C.G.Figdor
(2008).
Dendritic cell interaction with Candida albicans critically depends on N-linked mannan.
|
| |
J Biol Chem,
283,
20590-20599.
|
|
|
|
|
|
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A.D.Regan,
and
G.R.Whittaker
(2008).
Utilization of DC-SIGN for entry of feline coronaviruses into host cells.
|
| |
J Virol,
82,
11992-11996.
|
|
|
|
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|
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A.K.Azad,
J.B.Torrelles,
and
L.S.Schlesinger
(2008).
Mutation in the DC-SIGN cytoplasmic triacidic cluster motif markedly attenuates receptor activity for phagocytosis and endocytosis of mannose-containing ligands by human myeloid cells.
|
| |
J Leukoc Biol,
84,
1594-1603.
|
|
|
|
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|
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A.Rathore,
A.Chatterjee,
P.Sivarama,
N.Yamamoto,
and
T.N.Dhole
(2008).
Role of Homozygous DC-SIGNR 5/5 Tandem Repeat Polymorphism in HIV-1 Exposed Seronegative North Indian Individuals.
|
| |
J Clin Immunol,
28,
50-57.
|
|
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C.A.Aarnoudse,
M.Bax,
M.Sánchez-Hernández,
J.J.García-Vallejo,
and
Y.van Kooyk
(2008).
Glycan modification of the tumor antigen gp100 targets DC-SIGN to enhance dendritic cell induced antigen presentation to T cells.
|
| |
Int J Cancer,
122,
839-846.
|
|
|
|
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|
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C.K.Tang,
K.C.Sheng,
V.Apostolopoulos,
and
G.A.Pietersz
(2008).
Protein/peptide and DNA vaccine delivery by targeting C-type lectin receptors.
|
| |
Expert Rev Vaccines,
7,
1005-1018.
|
|
|
|
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|
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E.W.Adams,
D.M.Ratner,
P.H.Seeberger,
and
N.Hacohen
(2008).
Carbohydrate-mediated targeting of antigen to dendritic cells leads to enhanced presentation of antigen to T cells.
|
| |
Chembiochem,
9,
294-303.
|
|
|
|
|
|
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G.Cannon,
Y.Yi,
H.Ni,
E.Stoddard,
D.A.Scales,
D.I.Van Ryk,
I.Chaiken,
D.Malamud,
and
D.Weissman
(2008).
HIV envelope binding by macrophage-expressed gp340 promotes HIV-1 infection.
|
| |
J Immunol,
181,
2065-2070.
|
|
|
|
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|
|
J.Angulo,
I.Díaz,
J.J.Reina,
G.Tabarani,
F.Fieschi,
J.Rojo,
and
P.M.Nieto
(2008).
Saturation transfer difference (STD) NMR spectroscopy characterization of dual binding mode of a mannose disaccharide to DC-SIGN.
|
| |
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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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