2bbp

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{{Seed}}
 
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[[Image:2bbp.png|left|200px]]
 
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==NMR structures of the peptide linked to the genome (VPg) of poliovirus==
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The line below this paragraph, containing "STRUCTURE_2bbp", creates the "Structure Box" on the page.
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<StructureSection load='2bbp' size='340' side='right'caption='[[2bbp]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2bbp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_poliovirus_1_Mahoney Human poliovirus 1 Mahoney]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BBP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BBP FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bbp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bbp OCA], [https://pdbe.org/2bbp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bbp RCSB], [https://www.ebi.ac.uk/pdbsum/2bbp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bbp ProSAT]</span></td></tr>
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{{STRUCTURE_2bbp| PDB=2bbp | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/POLG_POL1M POLG_POL1M] 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 interaction of five VP1 proteins in the fivefold axes results in a prominent protusion extending to about 25 Angstroms from the capsid shell. The resulting structure appears as a steep plateau encircled by a valley or cleft. This depression also termed canyon is the receptor binding site. The capsid interacts with human PVR at this site to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis in Hela cells and through caveolin-mediated endocytosis in brain microvascular endothelial cells. VP4 and VP1 subsequently undergo conformational changes leading to the formation of a pore in the endosomal membrane, thereby delivering the viral genome into the cytoplasm.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> VP0 precursor is a component of immature procapsids (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities.<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 3A, via its hydrophobic domain, serves as membrane anchor. It also inhibits endoplasmic reticulum-to-Golgi transport (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> Protein 3C is a 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 co-operatively to the protease (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref> RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).<ref>PMID:9755863</ref> <ref>PMID:15919927</ref> <ref>PMID:18191571</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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VPgs are essential for replication of picornaviruses, which cause diseases such as poliomyelitis, foot and mouth disease, and the common cold. VPg in infected cells is covalently linked to the 5' end of the viral RNA, or, in a uridylylated form, free in the cytoplasm. We show here the first solution structure for a picornaviral VPg, that of the 22-residue peptide from poliovirus serotype 1. VPg in buffer is inherently flexible, but a single conformer was obtained by adding trimethylamine N-oxide (TMAO). TMAO had only minor effects on the TOCSY spectrum. However, it increased the amount of structured peptide, as indicated by more peaks in the NOESY spectrum and an up to 300% increase in the ratio of normalized NOE cross peak intensities to that in buffer. The data for VPg in TMAO yielded a well defined structure bundle with 0.6 A RMSD (versus 6.6 A in buffer alone), with 10-30 unambiguous constraints per residue. The structure consists of a large loop region from residues 1 to 14, from which the reactive tyrosinate projects outward, and a C-terminal helix from residues 18 to 21 that aligns the sidechains of conserved residues on one face. The structure has a stable docking position at an area on the poliovirus polymerase crystal structure identified as a VPg binding site by mutagenesis studies. Further, UTP and ATP dock in a base-specific manner to the reactive face of VPg, held in place by residues conserved in all picornavirus VPgs.
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===NMR structures of the peptide linked to the genome (VPg) of poliovirus===
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NMR structure of the viral peptide linked to the genome (VPg) of poliovirus.,Schein CH, Oezguen N, Volk DE, Garimella R, Paul A, Braun W Peptides. 2006 Jul;27(7):1676-84. Epub 2006 Mar 15. PMID:16540201<ref>PMID:16540201</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The line below this paragraph, {{ABSTRACT_PUBMED_16540201}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2bbp" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 16540201 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_16540201}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Human poliovirus 1 Mahoney]]
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2BBP is a [[Single protein]] structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BBP OCA].
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[[Category: Large Structures]]
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[[Category: Oezguen N]]
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==Reference==
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[[Category: Schein CH]]
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NMR structure of the viral peptide linked to the genome (VPg) of poliovirus., Schein CH, Oezguen N, Volk DE, Garimella R, Paul A, Braun W, Peptides. 2006 Jul;27(7):1676-84. Epub 2006 Mar 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16540201 16540201]
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Novel, structure-based mechanism for uridylylation of the genome-linked peptide (VPg) of picornaviruses., Schein CH, Volk DE, Oezguen N, Paul A, Proteins. 2006 Jun 1;63(4):719-26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16498624 16498624]
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[[Category: Single protein]]
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[[Category: Oezguen, N.]]
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[[Category: Schein, C H.]]
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[[Category: Flexible structure]]
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[[Category: Picornavirus]]
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[[Category: Rna transcription primer]]
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[[Category: Viral polymerase]]
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[[Category: Vpg]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:22:42 2008''
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Current revision

NMR structures of the peptide linked to the genome (VPg) of poliovirus

PDB ID 2bbp

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