2rdk

From Proteopedia

(Difference between revisions)

Current revision

Five site mutated Cyanovirin-N with Mannose dimer bound

Structural highlights

2rdk is a 2 chain structure with sequence from Nostoc ellipsosporum. 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

CVN_NOSEL Mannose-binding lectin.^[1] ^[2]

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

Cyanovirin (CV-N) is a small lectin with potent HIV neutralization activity, which could be exploited for a mucosal defense against HIV infection. The wild-type (wt) protein binds with high affinity to mannose-rich oligosaccharides on the surface of gp120 through two quasi-symmetric sites, located in domains A and B. We recently reported on a mutant of CV-N that contained a single functional mannose-binding site, domain B, showing that multivalent binding to oligomannosides is necessary for antiviral activity. The structure of the complex with dimannose determined at 1.8 A resolution revealed a different conformation of the binding site than previously observed in the NMR structure of wt CV-N. Here, we present the 1.35 A resolution structure of the complex, which traps three different binding conformations of the site and provides experimental support for a locking and gating mechanism in the nanoscale time regime observed by molecular dynamics simulations.

Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 A resolution.,Fromme R, Katiliene Z, Fromme P, Ghirlanda G Protein Sci. 2008 May;17(5):939-44. PMID:18436959^[3]

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

References

↑ Boyd MR, Gustafson KR, McMahon JB, Shoemaker RH, O'Keefe BR, Mori T, Gulakowski RJ, Wu L, Rivera MI, Laurencot CM, Currens MJ, Cardellina JH 2nd, Buckheit RW Jr, Nara PL, Pannell LK, Sowder RC 2nd, Henderson LE. Discovery of cyanovirin-N, a novel human immunodeficiency virus-inactivating protein that binds viral surface envelope glycoprotein gp120: potential applications to microbicide development. Antimicrob Agents Chemother. 1997 Jul;41(7):1521-30. PMID:9210678
↑ Botos I, Wlodawer A. Cyanovirin-N: a sugar-binding antiviral protein with a new twist. Cell Mol Life Sci. 2003 Feb;60(2):277-87. PMID:12678493
↑ Fromme R, Katiliene Z, Fromme P, Ghirlanda G. Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 A resolution. Protein Sci. 2008 May;17(5):939-44. PMID:18436959 doi:17/5/939

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/2rdk"

@@ Line 3: / Line 3: @@
 <StructureSection load='2rdk' size='340' side='right'caption='[[2rdk]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rdk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anabaena_variabilis_var._ellipsospora Anabaena variabilis var. ellipsospora]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rdk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc_ellipsosporum Nostoc ellipsosporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDK FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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;'>[[2pys|2pys]], [[2z21|2z21]], [[1lom|1lom]], [[1m5m|1m5m]], [[1iiy|1iiy]], [[3ezm|3ezm]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PRD_900111:2alpha-alpha-mannobiose'>PRD_900111</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=2rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdk OCA], [https://pdbe.org/2rdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdk RCSB], [https://www.ebi.ac.uk/pdbsum/2rdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdk ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/CVN_NOSEL CVN_NOSEL]] Mannose-binding lectin.<ref>PMID:9210678</ref> <ref>PMID:12678493</ref>
+[https://www.uniprot.org/uniprot/CVN_NOSEL CVN_NOSEL] Mannose-binding lectin.<ref>PMID:9210678</ref> <ref>PMID:12678493</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdk_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 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Anabaena variabilis var. ellipsospora]]
 [[Category: Large Structures]]
-[[Category: Fromme, P]]
+[[Category: Nostoc ellipsosporum]]
-[[Category: Fromme, R]]
+[[Category: Fromme P]]
-[[Category: Ghirlanda, G]]
+[[Category: Fromme R]]
-[[Category: Katiliene, Z]]
+[[Category: Ghirlanda G]]
-[[Category: Anti hiv]]
+[[Category: Katiliene Z]]
-[[Category: Antiviral protein]]
-[[Category: Cyanovirin-n]]
-[[Category: Protein synthesis inhibitor]]
-[[Category: Sugar binding protein]]

2rdk

From Proteopedia

Current revision

Five site mutated Cyanovirin-N with Mannose dimer bound

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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