2xr6

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo trimannoside mimic.

Structural highlights

2xr6 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.35Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CD209_HUMAN Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

Publication Abstract from PubMed

DC-SIGN is a dendritic cell-specific C-type lectin receptor that recognizes highly glycosylated ligands expressed on the surface of various pathogens. This receptor plays an important role in the early stages of many viral infections, including HIV, which makes it an interesting therapeutic target. Glycomimetic compounds are good drug candidates for DC-SIGN inhibition due to their high solubility, resistance to glycosidases, and nontoxicity. We studied the structural properties of the interaction of the tetrameric DC-SIGN extracellular domain (ECD), with two glycomimetic antagonists, a pseudomannobioside (1) and a linear pseudomannotrioside (2). Though the inhibitory potency of 2, as measured by SPR competition experiments, was 1 order of magnitude higher than that of 1, crystal structures of the complexes within the DC-SIGN carbohydrate recognition domain showed the same binding mode for both compounds. Moreover, when conjugated to multivalent scaffolds, the inhibitory potencies of these compounds became uniform. Combining isothermal titration microcalorimetry, analytical ultracentrifugation, and dynamic light scattering techniques to study DC-SIGN ECD interaction with these glycomimetics revealed that 2 is able, without any multivalent presentation, to cluster DC-SIGN tetramers leading to an artificially overestimated inhibitory potency. The use of multivalent scaffolds presenting 1 or 2 in HIV trans-infection inhibition assay confirms the loss of potency of 2 upon conjugation and the equal efficacy of chemically simpler compound 1. This study documents a unique case where, among two active compounds chemically derived, the compound with the lower apparent activity is the optimal lead for further drug development.

Unique DC-SIGN Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design.,Sutkeviciute I, Thepaut M, Sattin S, Berzi A, McGeagh J, Grudinin S, Weiser J, Le Roy A, Reina JJ, Rojo J, Clerici M, Bernardi A, Ebel C, Fieschi F ACS Chem Biol. 2014 May 6. PMID:24749535^[13]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Geijtenbeek TB, Kwon DS, Torensma R, van Vliet SJ, van Duijnhoven GC, Middel J, Cornelissen IL, Nottet HS, KewalRamani VN, Littman DR, Figdor CG, van Kooyk Y. DC-SIGN, a dendritic cell-specific HIV-1-binding protein that enhances trans-infection of T cells. Cell. 2000 Mar 3;100(5):587-97. PMID:10721995
↑ Geijtenbeek TB, Krooshoop DJ, Bleijs DA, van Vliet SJ, van Duijnhoven GC, Grabovsky V, Alon R, Figdor CG, van Kooyk Y. DC-SIGN-ICAM-2 interaction mediates dendritic cell trafficking. Nat Immunol. 2000 Oct;1(4):353-7. PMID:11017109 doi:10.1038/79815
↑ Engering A, Geijtenbeek TB, van Vliet SJ, Wijers M, van Liempt E, Demaurex N, Lanzavecchia A, Fransen J, Figdor CG, Piguet V, van Kooyk Y. The dendritic cell-specific adhesion receptor DC-SIGN internalizes antigen for presentation to T cells. J Immunol. 2002 Mar 1;168(5):2118-26. PMID:11859097
↑ Kwon DS, Gregorio G, Bitton N, Hendrickson WA, Littman DR. DC-SIGN-mediated internalization of HIV is required for trans-enhancement of T cell infection. Immunity. 2002 Jan;16(1):135-44. PMID:11825572
↑ Nobile C, Moris A, Porrot F, Sol-Foulon N, Schwartz O. Inhibition of human immunodeficiency virus type 1 Env-mediated fusion by DC-SIGN. J Virol. 2003 May;77(9):5313-23. PMID:12692233
↑ Appelmelk BJ, van Die I, van Vliet SJ, Vandenbroucke-Grauls CM, Geijtenbeek TB, van Kooyk Y. Cutting edge: carbohydrate profiling identifies new pathogens that interact with dendritic cell-specific ICAM-3-grabbing nonintegrin on dendritic cells. J Immunol. 2003 Feb 15;170(4):1635-9. PMID:12574325
↑ Geijtenbeek TB, Kwon DS, Torensma R, van Vliet SJ, van Duijnhoven GC, Middel J, Cornelissen IL, Nottet HS, KewalRamani VN, Littman DR, Figdor CG, van Kooyk Y. DC-SIGN, a dendritic cell-specific HIV-1-binding protein that enhances trans-infection of T cells. Cell. 2000 Mar 3;100(5):587-97. PMID:10721995
↑ Geijtenbeek TB, Krooshoop DJ, Bleijs DA, van Vliet SJ, van Duijnhoven GC, Grabovsky V, Alon R, Figdor CG, van Kooyk Y. DC-SIGN-ICAM-2 interaction mediates dendritic cell trafficking. Nat Immunol. 2000 Oct;1(4):353-7. PMID:11017109 doi:10.1038/79815
↑ Engering A, Geijtenbeek TB, van Vliet SJ, Wijers M, van Liempt E, Demaurex N, Lanzavecchia A, Fransen J, Figdor CG, Piguet V, van Kooyk Y. The dendritic cell-specific adhesion receptor DC-SIGN internalizes antigen for presentation to T cells. J Immunol. 2002 Mar 1;168(5):2118-26. PMID:11859097
↑ Kwon DS, Gregorio G, Bitton N, Hendrickson WA, Littman DR. DC-SIGN-mediated internalization of HIV is required for trans-enhancement of T cell infection. Immunity. 2002 Jan;16(1):135-44. PMID:11825572
↑ Nobile C, Moris A, Porrot F, Sol-Foulon N, Schwartz O. Inhibition of human immunodeficiency virus type 1 Env-mediated fusion by DC-SIGN. J Virol. 2003 May;77(9):5313-23. PMID:12692233
↑ Appelmelk BJ, van Die I, van Vliet SJ, Vandenbroucke-Grauls CM, Geijtenbeek TB, van Kooyk Y. Cutting edge: carbohydrate profiling identifies new pathogens that interact with dendritic cell-specific ICAM-3-grabbing nonintegrin on dendritic cells. J Immunol. 2003 Feb 15;170(4):1635-9. PMID:12574325
↑ Sutkeviciute I, Thepaut M, Sattin S, Berzi A, McGeagh J, Grudinin S, Weiser J, Le Roy A, Reina JJ, Rojo J, Clerici M, Bernardi A, Ebel C, Fieschi F. Unique DC-SIGN Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design. ACS Chem Biol. 2014 May 6. PMID:24749535 doi:http://dx.doi.org/10.1021/cb500054h

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xr6"

@@ Line 3: / Line 3: @@
 <StructureSection load='2xr6' size='340' side='right'caption='[[2xr6]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xr6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XR6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xr6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XR6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=AE9:2-AZIDOETHANOL'>AE9</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b6b|2b6b]], [[1sl4|1sl4]], [[1k9i|1k9i]], [[1sl5|1sl5]], [[2xr5|2xr5]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=07B:DIMETHYL+(1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE'>07B</scene>, <scene name='pdbligand=AE9:2-AZIDOETHANOL'>AE9</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xr6 OCA], [https://pdbe.org/2xr6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xr6 RCSB], [https://www.ebi.ac.uk/pdbsum/2xr6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xr6 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN]] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>   On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>
+[https://www.uniprot.org/uniprot/CD209_HUMAN CD209_HUMAN] Pathogen-recognition receptor expressed on the surface of immature dendritic cells (DCs) and involved in initiation of primary immune response. Thought to mediate the endocytosis of pathogens which are subsequently degraded in lysosomal compartments. The receptor returns to the cell membrane surface and the pathogen-derived antigens are presented to resting T-cells via MHC class II proteins to initiate the adaptive immune response. Probably recognizes in a calcium-dependent manner high mannose N-linked oligosaccharides in a variety of pathogen antigens, including HIV-1 gp120, HIV-2 gp120, SIV gp120, ebolavirus glycoproteins, cytomegalovirus gB, HCV E2, dengue virus gE, Leishmania pifanoi LPG, Lewis-x antigen in Helicobacter pylori LPS, mannose in Klebsiella pneumonae LPS, di-mannose and tri-mannose in Mycobacterium tuberculosis ManLAM and Lewis-x antigen in Schistosoma mansoni SEA.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>   On DCs it is a high affinity receptor for ICAM2 and ICAM3 by binding to mannose-like carbohydrates. May act as a DC rolling receptor that mediates transendothelial migration of DC presursors from blood to tissues by binding endothelial ICAM2. Seems to regulate DC-induced T-cell proliferation by binding to ICAM3 on T-cells in the immunological synapse formed between DC and T-cells.<ref>PMID:10721995</ref> <ref>PMID:11017109</ref> <ref>PMID:11859097</ref> <ref>PMID:11825572</ref> <ref>PMID:12692233</ref> <ref>PMID:12574325</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Bernardi, A]]
+[[Category: Bernardi A]]
-[[Category: Fieschi, F]]
+[[Category: Fieschi F]]
-[[Category: Reina, J]]
+[[Category: Reina J]]
-[[Category: Sattin, S]]
+[[Category: Sattin S]]
-[[Category: Suitkeviciute, I]]
+[[Category: Suitkeviciute I]]
-[[Category: Thepaut, M]]
+[[Category: Thepaut M]]
-[[Category: Carbohydrate binding]]
-[[Category: Mannose]]
-[[Category: Sugar binding protein]]

2xr6

From Proteopedia

Current revision

Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo trimannoside mimic.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox