1oda

From Proteopedia

(Difference between revisions)

Current revision

N-terminal of Sialoadhesin in complex with Me-a-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP compound)

Structural highlights

1oda is a 1 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.31Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SN_MOUSE Acts as an endocytic receptor mediating clathrin dependent endocytosis. Macrophage-restricted adhesion molecule that mediates sialic-acid dependent binding to lymphocytes, including granulocytes, monocytes, natural killer cells, B-cells and CD8 T-cells (By similarity). Preferentially binds to alpha-2,3-linked sialic acid. Binds to SPN/CD43 on T-cells. May play a role in hematopoiesis. May act as a counter-receptor for CLEC10A in lymph node.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Siglec family of receptors mediates cell surface interactions through recognition of sialylated glycoconjugates. The crystal structure of the N-terminal immunoglobulin-like domain of the Siglec sialoadhesin (SnD1) in complex with 2,3-sialyllactose has informed the design of sialic acid analogs (sialosides) that bind Siglecs with significantly enhanced affinities and specificities. Binding assays against sialoadhesin (Sn; Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4) show a 10- to 300-fold reduction in IC(50) values (relative to methyl-alpha-Neu5Ac) for three sialosides bearing aromatic group modifications of the glycerol side chain: Me-alpha-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ), Me-alpha-9-N-(naphthyl-2-carbonyl)-amino-9-deoxy-Neu5Ac (NAP), and Me-alpha-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP). Crystal structures of these sialosides in complex with SnD1 suggest explanations for the differences in specificity and affinity, providing further ideas for compound design of physiological and potentially therapeutic relevance.

Structure-guided design of sialic acid-based Siglec inhibitors and crystallographic analysis in complex with sialoadhesin.,Zaccai NR, Maenaka K, Maenaka T, Crocker PR, Brossmer R, Kelm S, Jones EY Structure. 2003 May;11(5):557-67. PMID:12737821^[2]

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

References

↑ Kumamoto Y, Higashi N, Denda-Nagai K, Tsuiji M, Sato K, Crocker PR, Irimura T. Identification of sialoadhesin as a dominant lymph node counter-receptor for mouse macrophage galactose-type C-type lectin 1. J Biol Chem. 2004 Nov 19;279(47):49274-80. Epub 2004 Sep 13. PMID:15364954 doi:http://dx.doi.org/10.1074/jbc.M409300200
↑ Zaccai NR, Maenaka K, Maenaka T, Crocker PR, Brossmer R, Kelm S, Jones EY. Structure-guided design of sialic acid-based Siglec inhibitors and crystallographic analysis in complex with sialoadhesin. Structure. 2003 May;11(5):557-67. PMID:12737821

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1oda"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1oda.png|left|200px]]
-<!--
+==N-terminal of Sialoadhesin in complex with Me-a-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP compound)==
-The line below this paragraph, containing "STRUCTURE_1oda", creates the "Structure Box" on the page.
+<StructureSection load='1oda' size='340' side='right'caption='[[1oda]], [[Resolution|resolution]] 3.31&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1oda]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.31&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BDU:ME-A-9-N-(BIPHENYL-4-CARBONYL)-AMINO-9-DEOXY-NEU5AC'>BDU</scene></td></tr>
-{{STRUCTURE_1oda|  PDB=1oda  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oda OCA], [https://pdbe.org/1oda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oda RCSB], [https://www.ebi.ac.uk/pdbsum/1oda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oda ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SN_MOUSE SN_MOUSE] Acts as an endocytic receptor mediating clathrin dependent endocytosis. Macrophage-restricted adhesion molecule that mediates sialic-acid dependent binding to lymphocytes, including granulocytes, monocytes, natural killer cells, B-cells and CD8 T-cells (By similarity). Preferentially binds to alpha-2,3-linked sialic acid. Binds to SPN/CD43 on T-cells. May play a role in hematopoiesis. May act as a counter-receptor for CLEC10A in lymph node.<ref>PMID:15364954</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/od/1oda_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oda ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Siglec family of receptors mediates cell surface interactions through recognition of sialylated glycoconjugates. The crystal structure of the N-terminal immunoglobulin-like domain of the Siglec sialoadhesin (SnD1) in complex with 2,3-sialyllactose has informed the design of sialic acid analogs (sialosides) that bind Siglecs with significantly enhanced affinities and specificities. Binding assays against sialoadhesin (Sn; Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4) show a 10- to 300-fold reduction in IC(50) values (relative to methyl-alpha-Neu5Ac) for three sialosides bearing aromatic group modifications of the glycerol side chain: Me-alpha-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ), Me-alpha-9-N-(naphthyl-2-carbonyl)-amino-9-deoxy-Neu5Ac (NAP), and Me-alpha-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP). Crystal structures of these sialosides in complex with SnD1 suggest explanations for the differences in specificity and affinity, providing further ideas for compound design of physiological and potentially therapeutic relevance.
-===N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH ME-A-9-N-(BIPHENYL-4-CARBONYL)-AMINO-9-DEOXY-NEU5AC (BIP COMPOUND)===
+Structure-guided design of sialic acid-based Siglec inhibitors and crystallographic analysis in complex with sialoadhesin.,Zaccai NR, Maenaka K, Maenaka T, Crocker PR, Brossmer R, Kelm S, Jones EY Structure. 2003 May;11(5):557-67. PMID:12737821<ref>PMID:12737821</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12737821}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1oda" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12737821 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12737821}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-ODA is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODA OCA].
-==Reference==
-<ref group="xtra">PMID:12737821</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Brossmer, R.]]
+[[Category: Brossmer R]]
-[[Category: Crocker, P R.]]
+[[Category: Crocker PR]]
-[[Category: Jones, E Y.]]
+[[Category: Jones EY]]
-[[Category: Kelm, S.]]
+[[Category: Kelm S]]
-[[Category: Maenaka, K.]]
+[[Category: Maenaka K]]
-[[Category: Maenaka, T.]]
+[[Category: Maenaka T]]
-[[Category: Zaccai, N R.]]
+[[Category: Zaccai NR]]
-[[Category: Carbohydrate binding]]
-[[Category: Cell adhesion]]
-[[Category: Immune system]]
-[[Category: Immunoglobulin superfamily]]
-[[Category: Inhibitor design]]
-[[Category: Siglec]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:05:13 2009''

1oda

From Proteopedia

Current revision

N-terminal of Sialoadhesin in complex with Me-a-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP compound)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox