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1qqp

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Revision as of 08:04, 28 February 2018

FOOT-AND-MOUTH DISEASE VIRUS/ OLIGOSACCHARIDE RECEPTOR COMPLEX.

Structural highlights

1qqp is a 4 chain structure with sequence from Foot-and-mouth disease virus. This structure supersedes the now removed PDB entry 1fhp. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[POLG_FMDVO] The leader protease autocatalytically cleaves itself from the polyprotein at the L/VP0 junction. It also cleaves the host translation initiation factor EIF4G1 and EIF4G3, in order to shut down the capped cellular mRNA transcription.^[1] ^[2] ^[3] ^[4] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes. The capsid interacts with host heparan sulfate and various integrins (alphavbeta6, alphavbeta1, alphavbeta3, alpha5beta1, alphavbeta8) to provide virion attachment to target Attachment via host integrins induces virion internalization predominantly through clathrin-mediated endocytosis. In strains adapted to cell culture, attachment to heparan sulfate can also be used and induces virion internalization through clathrin- and caveolin-independent endocytosis.^[5] ^[6] ^[7] ^[8] Protein VP0: VP0 precursor is a component of immature procapsids (By similarity).^[9] ^[10] ^[11] ^[12] Protein 2B: Affects membrane integrity and cause an increase in membrane permeability (By similarity).^[13] ^[14] ^[15] ^[16] Protein 2C: Associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).^[17] ^[18] ^[19] ^[20] Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).^[21] ^[22] ^[23] ^[24] Protein 3B-1, 3B-2 and 3B-3 are covalently linked to the 5'-end of both the positive-strand and negative-strand genomic RNAs. They acts as a genome-linked replication primer (By similarity).^[25] ^[26] ^[27] ^[28] Protease 3C: cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind cooperatively to the protease (By similarity).^[29] ^[30] ^[31] ^[32] RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).^[33] ^[34] ^[35] ^[36]

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

Heparan sulfate has an important role in cell entry by foot-and-mouth disease virus (FMDV). We find that subtype O1 FMDV binds this glycosaminoglycan with a high affinity by immobilizing a specific highly abundant motif of sulfated sugars. The binding site is a shallow depression on the virion surface, located at the junction of the three major capsid proteins, VP1, VP2 and VP3. Two pre-formed sulfate-binding sites control receptor specificity. Residue 56 of VP3, an arginine in this virus, is critical to this recognition, forming a key component of both sites. This residue is a histidine in field isolates of the virus, switching to an arginine in adaptation to tissue culture, forming the high affinity heparan sulfate-binding site. We postulate that this site is a conserved feature of FMDVs, such that in the infected animal there is a biological advantage to low affinity, or more selective, interactions with glycosaminoglycan receptors.

The structure and function of a foot-and-mouth disease virus-oligosaccharide receptor complex.,Fry EE, Lea SM, Jackson T, Newman JW, Ellard FM, Blakemore WE, Abu-Ghazaleh R, Samuel A, King AM, Stuart DI EMBO J. 1999 Feb 1;18(3):543-54. PMID:9927414^[37]

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

References

↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Medina M, Domingo E, Brangwyn JK, Belsham GJ. The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology. 1993 May;194(1):355-9. PMID:8386879 doi:http://dx.doi.org/S0042-6822(83)71267-5
↑ Glaser W, Skern T. Extremely efficient cleavage of eIF4G by picornaviral proteinases L and 2A in vitro. FEBS Lett. 2000 Sep 1;480(2-3):151-5. PMID:11034318
↑ Gradi A, Foeger N, Strong R, Svitkin YV, Sonenberg N, Skern T, Belsham GJ. Cleavage of eukaryotic translation initiation factor 4GII within foot-and-mouth disease virus-infected cells: identification of the L-protease cleavage site in vitro. J Virol. 2004 Apr;78(7):3271-8. PMID:15016848
↑ O'Donnell V, Larocco M, Baxt B. Heparan sulfate-binding foot-and-mouth disease virus enters cells via caveola-mediated endocytosis. J Virol. 2008 Sep;82(18):9075-85. doi: 10.1128/JVI.00732-08. Epub 2008 Jul 9. PMID:18614639 doi:http://dx.doi.org/10.1128/JVI.00732-08
↑ Fry EE, Lea SM, Jackson T, Newman JW, Ellard FM, Blakemore WE, Abu-Ghazaleh R, Samuel A, King AM, Stuart DI. The structure and function of a foot-and-mouth disease virus-oligosaccharide receptor complex. EMBO J. 1999 Feb 1;18(3):543-54. PMID:9927414 doi:http://dx.doi.org/10.1093/emboj/18.3.543

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/1qqp"

@@ Line 1: / Line 1: @@
 ==FOOT-AND-MOUTH DISEASE VIRUS/ OLIGOSACCHARIDE RECEPTOR COMPLEX.==
 <StructureSection load='1qqp' size='340' side='right' caption='[[1qqp]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qqp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Fmdv Fmdv]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fhp 1fhp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qqp]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Foot-and-mouth_disease_virus Foot-and-mouth disease virus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fhp 1fhp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1QQP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QQP FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IDS:2-O-SULFO-ALPHA-L-IDOPYRANURONIC+ACID'>IDS</scene>, <scene name='pdbligand=IDX:2-O-SULFO-ALPHA-L-GULOPYRANURONIC+ACID'>IDX</scene>, <scene name='pdbligand=SGN:N,O6-DISULFO-GLUCOSAMINE'>SGN</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=1qqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqp OCA], [http://pdbe.org/1qqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qqp RCSB], [http://www.ebi.ac.uk/pdbsum/1qqp PDBsum]</span></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=1qqp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qqp OCA], [http://pdbe.org/1qqp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1qqp RCSB], [http://www.ebi.ac.uk/pdbsum/1qqp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1qqp ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 12: / Line 13: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/1qqp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qq/1qqp_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qqp ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Fmdv]]
+[[Category: Foot-and-mouth disease virus]]
 [[Category: Abu-Ghazaleh, R]]
 [[Category: Blakemore, W E]]

1qqp

From Proteopedia

Revision as of 08:04, 28 February 2018

FOOT-AND-MOUTH DISEASE VIRUS/ OLIGOSACCHARIDE RECEPTOR COMPLEX.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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