2qsk: Difference between revisions

Latest revision as of 11:40, 30 August 2023

Atomic-resolution crystal structure of the Recombinant form of Scytovirin

Structural highlights

2qsk is a 1 chain structure with sequence from Scytonema varium. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1Å
Ligands:	CL, GOL
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SVN_SCYVA Has strong anti-HIV activity against T-tropic strains of HIV-1 and weaker activity against M-tropic strains of HIV-1. Inhibits HIV-1 fusion and infection of CD4 LTR beta-gal cells in vitro. Inhibits fusion of HIV infected CEM-SS cells with uninfected CEM-SS cells, and fusion of HIV-1 Env expressing HL2/3 cells with CD4 LTR beta-gal cells. Binds to HIV gp120, HIV gp160 and to a lesser extent HIV gp41. Binding to HIV gp120 is glycosylation dependent. Binds with high specificity to the tetrasaccharide Man-alpha-1,2-Man-alpha-1,6-Man-alpha-1,6-Man and also binds the higher-order oligosaccharides oligomannose 8 and oligomannose 9. Does not bind to monosaccharides, complex or hybrid N-linked oligosaccharides or chitin.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The crystal structures of the natural and recombinant antiviral lectin scytovirin (SVN) were solved by single-wavelength anomalous scattering and refined with data extending to 1.3 A and 1.0 A resolution, respectively. A molecule of SVN consists of a single chain 95 amino acids long, with an almost perfect sequence repeat that creates two very similar domains (RMS deviation 0.25 A for 40 pairs of Calpha atoms). The crystal structure differs significantly from a previously published NMR structure of the same protein, with the RMS deviations calculated separately for the N- and C-terminal domains of 5.3 A and 3.7 A, respectively, and a very different relationship between the two domains. In addition, the disulfide bonding pattern of the crystal structures differs from that described in the previously published mass spectrometry and NMR studies.

Atomic-resolution crystal structure of the antiviral lectin scytovirin.,Moulaei T, Botos I, Ziolkowska NE, Bokesch HR, Krumpe LR, McKee TC, O'Keefe BR, Dauter Z, Wlodawer A Protein Sci. 2007 Dec;16(12):2756-60. Epub 2007 Oct 26. PMID:17965185^[5]

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

References

↑ Bokesch HR, O'Keefe BR, McKee TC, Pannell LK, Patterson GM, Gardella RS, Sowder RC 2nd, Turpin J, Watson K, Buckheit RW Jr, Boyd MR. A potent novel anti-HIV protein from the cultured cyanobacterium Scytonema varium. Biochemistry. 2003 Mar 11;42(9):2578-84. doi: 10.1021/bi0205698. PMID:12614152 doi:https://dx.doi.org/10.1021/bi0205698
↑ Xiong C, O'Keefe BR, Byrd RA, McMahon JB. Potent anti-HIV activity of scytovirin domain 1 peptide. Peptides. 2006 Jul;27(7):1668-75. doi: 10.1016/j.peptides.2006.03.018. Epub 2006 , May 2. PMID:16647158 doi:https://dx.doi.org/10.1016/j.peptides.2006.03.018
↑ Ratner DM, Seeberger PH. Carbohydrate microarrays as tools in HIV glycobiology. Curr Pharm Des. 2007;13(2):173-83. doi: 10.2174/138161207779313650. PMID:17269926 doi:https://dx.doi.org/10.2174/138161207779313650
↑ McFeeters RL, Xiong C, O'Keefe BR, Bokesch HR, McMahon JB, Ratner DM, Castelli R, Seeberger PH, Byrd RA. The novel fold of scytovirin reveals a new twist for antiviral entry inhibitors. J Mol Biol. 2007 Jun 1;369(2):451-61. Epub 2007 Mar 20. PMID:17434526 doi:https://dx.doi.org/S0022-2836(07)00371-3
↑ Moulaei T, Botos I, Ziolkowska NE, Bokesch HR, Krumpe LR, McKee TC, O'Keefe BR, Dauter Z, Wlodawer A. Atomic-resolution crystal structure of the antiviral lectin scytovirin. Protein Sci. 2007 Dec;16(12):2756-60. Epub 2007 Oct 26. PMID:17965185 doi:ps.073157507

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Bokesch HR, O'Keefe BR, McKee TC, Pannell LK, Patterson GM, Gardella RS, Sowder RC 2nd, Turpin J, Watson K, Buckheit RW Jr, Boyd MR. A potent novel anti-HIV protein from the cultured cyanobacterium Scytonema varium. Biochemistry. 2003 Mar 11;42(9):2578-84. doi: 10.1021/bi0205698. PMID:12614152 doi:https://dx.doi.org/10.1021/bi0205698

[2] Xiong C, O'Keefe BR, Byrd RA, McMahon JB. Potent anti-HIV activity of scytovirin domain 1 peptide. Peptides. 2006 Jul;27(7):1668-75. doi: 10.1016/j.peptides.2006.03.018. Epub 2006 , May 2. PMID:16647158 doi:https://dx.doi.org/10.1016/j.peptides.2006.03.018

[3] Ratner DM, Seeberger PH. Carbohydrate microarrays as tools in HIV glycobiology. Curr Pharm Des. 2007;13(2):173-83. doi: 10.2174/138161207779313650. PMID:17269926 doi:https://dx.doi.org/10.2174/138161207779313650

[4] McFeeters RL, Xiong C, O'Keefe BR, Bokesch HR, McMahon JB, Ratner DM, Castelli R, Seeberger PH, Byrd RA. The novel fold of scytovirin reveals a new twist for antiviral entry inhibitors. J Mol Biol. 2007 Jun 1;369(2):451-61. Epub 2007 Mar 20. PMID:17434526 doi:https://dx.doi.org/S0022-2836(07)00371-3

[5] Moulaei T, Botos I, Ziolkowska NE, Bokesch HR, Krumpe LR, McKee TC, O'Keefe BR, Dauter Z, Wlodawer A. Atomic-resolution crystal structure of the antiviral lectin scytovirin. Protein Sci. 2007 Dec;16(12):2756-60. Epub 2007 Oct 26. PMID:17965185 doi:ps.073157507

[1]

[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
 ==Atomic-resolution crystal structure of the Recombinant form of Scytovirin==
-<StructureSection load='2qsk' size='340' side='right' caption='[[2qsk]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
+<StructureSection load='2qsk' size='340' side='right'caption='[[2qsk]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qsk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Scytonema_varium Scytonema varium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QSK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QSK FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qsk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Scytonema_varium Scytonema varium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QSK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QSK FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
+</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&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qt4|2qt4]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qsk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qsk RCSB], [http://www.ebi.ac.uk/pdbsum/2qsk PDBsum]</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=2qsk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qsk OCA], [https://pdbe.org/2qsk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qsk RCSB], [https://www.ebi.ac.uk/pdbsum/2qsk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qsk ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SVN_SCYVA SVN_SCYVA] Has strong anti-HIV activity against T-tropic strains of HIV-1 and weaker activity against M-tropic strains of HIV-1. Inhibits HIV-1 fusion and infection of CD4 LTR beta-gal cells in vitro. Inhibits fusion of HIV infected CEM-SS cells with uninfected CEM-SS cells, and fusion of HIV-1 Env expressing HL2/3 cells with CD4 LTR beta-gal cells. Binds to HIV gp120, HIV gp160 and to a lesser extent HIV gp41. Binding to HIV gp120 is glycosylation dependent. Binds with high specificity to the tetrasaccharide Man-alpha-1,2-Man-alpha-1,6-Man-alpha-1,6-Man and also binds the higher-order oligosaccharides oligomannose 8 and oligomannose 9. Does not bind to monosaccharides, complex or hybrid N-linked oligosaccharides or chitin.<ref>PMID:12614152</ref> <ref>PMID:16647158</ref> <ref>PMID:17269926</ref> <ref>PMID:17434526</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2qsk" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Scytonema varium]]
-[[Category: Botos, I.]]
+[[Category: Botos I]]
-[[Category: Dauter, Z.]]
+[[Category: Dauter Z]]
-[[Category: Moulaei, T.]]
+[[Category: Moulaei T]]
-[[Category: Wlodawer, A.]]
+[[Category: Wlodawer A]]
-[[Category: Ziolkowska, N E.]]
+[[Category: Ziolkowska NE]]
-[[Category: Lectin]]
-[[Category: Sugar binding protein]]

2qsk: Difference between revisions

Latest revision as of 11:40, 30 August 2023

Atomic-resolution crystal structure of the Recombinant form of Scytovirin

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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