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4z9k

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Revision as of 15:55, 11 December 2019

Ricin A chain bound to camelid nanobody (VHH2)(F5)

Structural highlights

4z9k is a 2 chain structure with sequence from Alpaca and Castor bean. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	4lgp, 4lgr, 4lhj, 4lhq, 4lgs, 5boz
Activity:	rRNA N-glycosylase, with EC number 3.2.2.22
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RICI_RICCO] Ricin is highly toxic to animal cells and to a lesser extent to plant cells. The A chain acts as a glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. As this loop is involved in elongation factor binding, modified ribosomes are catalytically inactive and unable to support protein synthesis. The A chain can inactivate a few thousand ribosomes per minute, faster than the cell can make new ones. Therefore a single A chain molecule can kill an animal cell. The B chain binds to beta-D-galactopyranoside moieties on cell surface glycoproteins and glycolipids and facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (Lectin activity).

Publication Abstract from PubMed

In this report, we describe the X-ray crystal structures of two single domain camelid antibodies (VH H), F5 and F8, each in complex with ricin toxin's enzymatic subunit (RTA). F5 has potent toxin-neutralizing activity, while F8 has weak neutralizing activity. F5 buried a total of 1760 A(2) in complex with RTA and made contact with three prominent secondary structural elements: alpha-helix B (Residues 98-106), beta-strand h (Residues 113-117), and the C-terminus of alpha-helix D (Residues 154-156). F8 buried 1103 A(2) in complex with RTA that was centered primarily on beta-strand h. As such, the structural epitope of F8 is essentially nested within that of F5. All three of the F5 complementarity determining regions CDRs were involved in RTA contact, whereas F8 interactions were almost entirely mediated by CDR3, which essentially formed a seventh beta-strand within RTA's centrally located beta-sheet. A comparison of the two structures reported here to several previously reported (RTA-VH H) structures identifies putative contact sites on RTA, particularly alpha-helix B, associated with potent toxin-neutralizing activity. This information has implications for rational design of RTA-based subunit vaccines for biodefense. Proteins 2016; 84:1162-1172. (c) 2016 Wiley Periodicals, Inc.

Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit.,Rudolph MJ, Vance DJ, Cassidy MS, Rong Y, Shoemaker CB, Mantis NJ Proteins. 2016 Aug;84(8):1162-72. doi: 10.1002/prot.25062. Epub 2016 Jun 15. PMID:27159829^[1]

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

References

↑ Rudolph MJ, Vance DJ, Cassidy MS, Rong Y, Shoemaker CB, Mantis NJ. Structural analysis of nested neutralizing and non-neutralizing B cell epitopes on ricin toxin's enzymatic subunit. Proteins. 2016 Aug;84(8):1162-72. doi: 10.1002/prot.25062. Epub 2016 Jun 15. PMID:27159829 doi:http://dx.doi.org/10.1002/prot.25062

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4z9k"

@@ Line 3: / Line 3: @@
 <StructureSection load='4z9k' size='340' side='right'caption='[[4z9k]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4z9k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z9K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z9K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4z9k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Alpaca Alpaca] and [http://en.wikipedia.org/wiki/Castor_bean Castor bean]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z9K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z9K FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lgp|4lgp]], [[4lgr|4lgr]], [[4lhj|4lhj]], [[4lhq|4lhq]], [[4lgs|4lgs]], [[5boz|5boz]]</td></tr>
@@ Line 28: / Line 28: @@
 __TOC__
 </StructureSection>
+[[Category: Alpaca]]
+[[Category: Castor bean]]
 [[Category: Large Structures]]
 [[Category: RRNA N-glycosylase]]

4z9k

From Proteopedia

Revision as of 15:55, 11 December 2019

Ricin A chain bound to camelid nanobody (VHH2)(F5)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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