This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3c9z

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (11:16, 21 February 2024) (edit) (undo)
 
Line 4: Line 4:
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3c9z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sambucus_nigra Sambucus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C9Z FirstGlance]. <br>
<table><tr><td colspan='2'>[[3c9z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sambucus_nigra Sambucus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C9Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C9Z FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</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;'>[[3ca0|3ca0]], [[3ca1|3ca1]], [[3ca3|3ca3]], [[3ca4|3ca4]], [[3ca5|3ca5]], [[3ca6|3ca6]], [[3cah|3cah]]</div></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3c9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c9z OCA], [https://pdbe.org/3c9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c9z RCSB], [https://www.ebi.ac.uk/pdbsum/3c9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c9z ProSAT]</span></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=3c9z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c9z OCA], [https://pdbe.org/3c9z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c9z RCSB], [https://www.ebi.ac.uk/pdbsum/3c9z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c9z ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
-
[[https://www.uniprot.org/uniprot/NIGB_SAMNI NIGB_SAMNI]] Non-toxic type 2 RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain is a galactose-specific lectin that facilitates the binding of nigrin b to the cell membrane that precedes endocytosis.
+
[https://www.uniprot.org/uniprot/NIGB_SAMNI NIGB_SAMNI] Non-toxic type 2 RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain is a galactose-specific lectin that facilitates the binding of nigrin b to the cell membrane that precedes endocytosis.
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
Bark of elderberry (Sambucus nigra) contains a galactose (Gal)/N-acetylgalactosamine (GalNAc)-specific lectin (SNA-II) corresponding to slightly truncated B-chains of a genuine Type-II ribosome-inactivating protein (Type-II RIPs, SNA-V), found in the same species. The three-dimensional X-ray structure of SNA-II has been determined in two distinct crystal forms, hexagonal and tetragonal, at 1.90 A and 1.35 A, respectively. In both crystal forms, the SNA-II molecule folds into two linked betabeta-trefoil domains, with an overall conformation similar to that of the B-chains of ricin and other Type-II RIPs. Glycosylation is observed at four sites along the polypeptide chain, accounting for 14 saccharide units. The high-resolution structures of SNA-II in complex with Gal and five Gal-related saccharides (GalNAc, lactose, alphaalpha1-methylgalactose, fucose, and the carcinoma-specific Tn antigen) were determined at 1.55 A resolution or better. Binding is observed in two saccharide-binding sites for most of the sugars: a conserved aspartate residue interacts simultaneously with the O3 and O4 atoms of saccharides. In one of the binding sites, additional interactions with the protein involve the O6 atom. Analytical gel filtration, small angle X-ray scattering studies and crystal packing analysis indicate that, although some oligomeric species are present, the monomeric species predominate in solution. Proteins 2008. (c) 2008 Wiley-Liss, Inc.
+
-
 
+
-
Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra.,Maveyraud L, Niwa H, Guillet V, Svergun DI, Konarev PV, Palmer RA, Peumans WJ, Rouge P, Van Damme EJ, Reynolds CD, Mourey L Proteins. 2008 Sep 17. PMID:18798567<ref>PMID:18798567</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3c9z" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
*[[Agglutinin 3D structures|Agglutinin 3D structures]]
*[[Agglutinin 3D structures|Agglutinin 3D structures]]
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Sambucus nigra]]
[[Category: Sambucus nigra]]
-
[[Category: Guillet, V]]
+
[[Category: Guillet V]]
-
[[Category: Maveyraud, L]]
+
[[Category: Maveyraud L]]
-
[[Category: Mourey, L]]
+
[[Category: Mourey L]]
-
[[Category: Beta-trefoil]]
+
-
[[Category: Glycoprotein]]
+
-
[[Category: Glycosylation]]
+
-
[[Category: Lectin]]
+
-
[[Category: Plant protein]]
+
-
[[Category: Ricin-b domain]]
+
-
[[Category: Sugar binding protein]]
+

Current revision

Sambucus nigra agglutinin II (SNA-II), tetragonal crystal form

PDB ID 3c9z

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3c9z"
Personal tools