3ca5

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose

Structural highlights

3ca5 is a 1 chain structure with sequence from Sambucus nigra. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.55Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

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

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^[1]

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

References

↑ Maveyraud L, Niwa H, Guillet V, Svergun DI, Konarev PV, Palmer RA, Peumans WJ, Rouge P, Van Damme EJ, Reynolds CD, Mourey L. Structural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra. Proteins. 2008 Sep 17. PMID:18798567 doi:10.1002/prot.22222

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ca5"

Categories: Large Structures | Sambucus nigra | Maveyraud L | Mourey L

@@ Line 1: / Line 1: @@
 ==Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose==
-<StructureSection load='3ca5' size='340' side='right' caption='[[3ca5]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
+<StructureSection load='3ca5' size='340' side='right'caption='[[3ca5]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ca5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sambucus_nigra Sambucus nigra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CA5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CA5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ca5]] 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=3CA5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CA5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AMG:ALPHA-METHYL-D-GALACTOSIDE'>AMG</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]] 1.55&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3c9z|3c9z]], [[3ca0|3ca0]], [[3ca1|3ca1]], [[3ca3|3ca3]], [[3ca4|3ca4]], [[3ca6|3ca6]], [[3cah|3cah]]</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=AMG:ALPHA-METHYL-D-GALACTOSIDE'>AMG</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ca5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca5 OCA], [http://pdbe.org/3ca5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ca5 RCSB], [http://www.ebi.ac.uk/pdbsum/3ca5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ca5 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=3ca5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ca5 OCA], [https://pdbe.org/3ca5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ca5 RCSB], [https://www.ebi.ac.uk/pdbsum/3ca5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ca5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
 == 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/ca/3ca5_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ca/3ca5_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 3ca5" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Agglutinin 3D structures|Agglutinin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Sambucus nigra]]
-[[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: Signaling protein]]
-[[Category: Sugar binding protein]]

3ca5

From Proteopedia

Current revision

Crystal structure of Sambucus nigra agglutinin II (SNA-II)-tetragonal crystal form- complexed to alpha1 methylgalactose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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