5gka

From Proteopedia

(Difference between revisions)

Revision as of 11:34, 2 August 2023

cryo-EM structure of human Aichi virus

5gka, resolution 3.70Å

Structural highlights

5gka is a 3 chain structure with sequence from Aichi virus A846/88. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.7Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POLG_AIVA8 Required for viral RNA replication and viral RNA encapsidation (PubMed:14512530). Does not have any proteolytic activity (PubMed:14512530).^[1] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP0 and VP3 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).^[2] ^[3] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP1 and VP3 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).^[4] ^[5] Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP0 and VP1 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).^[6] ^[7] Required for viral RNA replication (PubMed:18653460). Does not have any proteolytic activity (PubMed:18653460).^[8] Affects membrane integrity and causes an increase in membrane permeability. Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3.[UniProtKB:P03300] Serves as membrane anchor via its hydrophobic domain. Plays an essential role in viral RNA replication by recruiting PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (PubMed:22124328, PubMed:24672044, PubMed:27989622, PubMed:30755512, PubMed:22258260). Stimulates the enzymatic activity of PI4KB, this activation is sensitized by ACBD3 (PubMed:24672044, PubMed:27989622).^[9] ^[10] ^[11] ^[12] ^[13] Forms a primer, VPg-pU, which is utilized by the polymerase for the initiation of RNA chains.[UniProtKB:P03304] Cysteine protease that generates mature viral proteins from the precursor polyprotein (By similarity). In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate cooperatively bind to the protease (By similarity).[UniProtKB:P03304][UniProtKB:P12296] Replicates the genomic and antigenomic RNAs by recognizing replications specific signals (By similarity). Performs VPg uridylylation (By similarity).[UniProtKB:P12296]

Publication Abstract from PubMed

Aichi virus (AiV), an unusual and poorly characterized picornavirus, classified in the genus Kobuvirus, can cause severe gastroenteritis and deaths in children below the age of five years, especially in developing countries(1,2). The seroprevalence of AiV is approximately 60% in children under the age of ten years and reaches 90% later in life(3,4). There is no available vaccine or effective antiviral treatment. Here, we describe the structure of AiV at 3.7 A. This first high-resolution structure for a kobuvirus is intermediate between those of the enteroviruses and cardioviruses, with a shallow, narrow depression bounded by the prominent VP0 CD loops (linking the C and D strands of the beta-barrel), replacing the depression known as the canyon, frequently the site of receptor attachment in enteroviruses. VP0 is not cleaved to form VP2 and VP4, so the 'VP2' beta-barrel structure is complemented with a unique extended structure on the inside of the capsid. On the outer surface, a polyproline helix structure, not seen previously in picornaviruses is present at the C terminus of VP1, a position where integrin binding motifs are found in some other picornaviruses. A peptide corresponding to this polyproline motif somewhat attenuates virus infectivity, presumably blocking host-cell attachment. This may guide cellular receptor identification.

Structure of human Aichi virus and implications for receptor binding.,Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320^[14]

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

References

↑ Sasaki J, Nagashima S, Taniguchi K. Aichi virus leader protein is involved in viral RNA replication and encapsidation. J Virol. 2003 Oct;77(20):10799-807. PMID:14512530 doi:10.1128/jvi.77.20.10799-10807.2003
↑ Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320 doi:http://dx.doi.org/10.1038/nmicrobiol.2016.150
↑ Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P. Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism. J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122 doi:http://dx.doi.org/10.1128/JVI.01601-16
↑ Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320 doi:http://dx.doi.org/10.1038/nmicrobiol.2016.150
↑ Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P. Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism. J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122 doi:http://dx.doi.org/10.1128/JVI.01601-16
↑ Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320 doi:http://dx.doi.org/10.1038/nmicrobiol.2016.150
↑ Sabin C, Fuzik T, Skubnik K, Palkova L, Lindberg AM, Plevka P. Structure of Aichi virus 1 and its empty particle: clues towards kobuvirus genome release mechanism. J Virol. 2016 Sep 28. pii: JVI.01601-16. PMID:27681122 doi:http://dx.doi.org/10.1128/JVI.01601-16
↑ Sasaki J, Taniguchi K. Aichi virus 2A protein is involved in viral RNA replication. J Virol. 2008 Oct;82(19):9765-9. PMID:18653460 doi:10.1128/JVI.01051-08
↑ Sasaki J, Ishikawa K, Arita M, Taniguchi K. ACBD3-mediated recruitment of PI4KB to picornavirus RNA replication sites. EMBO J. 2012 Feb 1;31(3):754-66. PMID:22124328 doi:10.1038/emboj.2011.429
↑ Greninger AL, Knudsen GM, Betegon M, Burlingame AL, Derisi JL. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ. J Virol. 2012 Apr;86(7):3605-16. PMID:22258260 doi:10.1128/JVI.06778-11
↑ Ishikawa-Sasaki K, Sasaki J, Taniguchi K. A complex comprising phosphatidylinositol 4-kinase IIIβ, ACBD3, and Aichi virus proteins enhances phosphatidylinositol 4-phosphate synthesis and is critical for formation of the viral replication complex. J Virol. 2014 Jun;88(12):6586-98. PMID:24672044 doi:10.1128/JVI.00208-14
↑ McPhail JA, Ottosen EH, Jenkins ML, Burke JE. The Molecular Basis of Aichi Virus 3A Protein Activation of Phosphatidylinositol 4 Kinase IIIbeta, PI4KB, through ACBD3. Structure. 2016 Dec 7. pii: S0969-2126(16)30358-6. doi:, 10.1016/j.str.2016.11.016. PMID:27989622 doi:http://dx.doi.org/10.1016/j.str.2016.11.016
↑ Lyoo H, van der Schaar HM, Dorobantu CM, Rabouw HH, Strating JRPM, van Kuppeveld FJM. ACBD3 Is an Essential Pan-enterovirus Host Factor That Mediates the Interaction between Viral 3A Protein and Cellular Protein PI4KB. mBio. 2019 Feb 12;10(1):e02742-18. PMID:30755512 doi:10.1128/mBio.02742-18
↑ Zhu L, Wang X, Ren J, Kotecha A, Walter TS, Yuan S, Yamashita T, Tuthill TJ, Fry EE, Rao Z, Stuart DI. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016 Sep 5;1:16150. doi: 10.1038/nmicrobiol.2016.150. PMID:27595320 doi:http://dx.doi.org/10.1038/nmicrobiol.2016.150

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5gka"

@@ Line 3: / Line 3: @@
 <SX load='5gka' size='340' side='right' viewer='molstar' caption='[[5gka]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gka]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GKA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gka]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aichi_virus_A846/88 Aichi virus A846/88]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKA FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5gka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gka OCA], [http://pdbe.org/5gka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gka RCSB], [http://www.ebi.ac.uk/pdbsum/5gka PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gka ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.7&#8491;</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=5gka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gka OCA], [https://pdbe.org/5gka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gka RCSB], [https://www.ebi.ac.uk/pdbsum/5gka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gka ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_AIVA8 POLG_AIVA8] Required for viral RNA replication and viral RNA encapsidation (PubMed:14512530). Does not have any proteolytic activity (PubMed:14512530).<ref>PMID:14512530</ref>   Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP0 and VP3 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).<ref>PMID:27595320</ref> <ref>PMID:27681122</ref>   Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP1 and VP3 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).<ref>PMID:27595320</ref> <ref>PMID:27681122</ref>   Forms an icosahedral capsid of pseudo T=3 symmetry with capsid proteins VP0 and VP1 (PubMed:27681122, PubMed:27595320). Together they form an icosahedral capsid composed of 60 copies of each VP0, VP1, and VP3 (PubMed:27681122, PubMed:27595320). All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll (PubMed:27595320).<ref>PMID:27595320</ref> <ref>PMID:27681122</ref>   Required for viral RNA replication (PubMed:18653460). Does not have any proteolytic activity (PubMed:18653460).<ref>PMID:18653460</ref>   Affects membrane integrity and causes an increase in membrane permeability.  Induces and associates with structural rearrangements of intracellular membranes. Displays RNA-binding, nucleotide binding and NTPase activities. May play a role in virion morphogenesis and viral RNA encapsidation by interacting with the capsid protein VP3.[UniProtKB:P03300]  Serves as membrane anchor via its hydrophobic domain. Plays an essential role in viral RNA replication by recruiting PI4KB at the viral replication sites, thereby allowing the formation of the rearranged membranous structures where viral replication takes place (PubMed:22124328, PubMed:24672044, PubMed:27989622, PubMed:30755512, PubMed:22258260). Stimulates the enzymatic activity of PI4KB, this activation is sensitized by ACBD3 (PubMed:24672044, PubMed:27989622).<ref>PMID:22124328</ref> <ref>PMID:22258260</ref> <ref>PMID:24672044</ref> <ref>PMID:27989622</ref> <ref>PMID:30755512</ref>   Forms a primer, VPg-pU, which is utilized by the polymerase for the initiation of RNA chains.[UniProtKB:P03304]  Cysteine protease that generates mature viral proteins from the precursor polyprotein (By similarity). In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate cooperatively bind to the protease (By similarity).[UniProtKB:P03304][UniProtKB:P12296]  Replicates the genomic and antigenomic RNAs by recognizing replications specific signals (By similarity). Performs VPg uridylylation (By similarity).[UniProtKB:P12296]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 22: @@
 __TOC__
 </SX>
+[[Category: Aichi virus A846/88]]
 [[Category: Large Structures]]
-[[Category: Fry, E E]]
+[[Category: Fry EE]]
-[[Category: Rao, Z H]]
+[[Category: Rao ZH]]
-[[Category: Ren, J S]]
+[[Category: Ren JS]]
-[[Category: Stuart, D I]]
+[[Category: Stuart DI]]
-[[Category: Tuthill, T J]]
+[[Category: Tuthill TJ]]
-[[Category: Wang, X X]]
+[[Category: Wang XX]]
-[[Category: Zhu, L]]
+[[Category: Zhu L]]
-[[Category: Entry]]
-[[Category: Gastroenteritis]]
-[[Category: Picornavirus]]
-[[Category: Receptor binding]]
-[[Category: Virus]]

5gka

From Proteopedia

Revision as of 11:34, 2 August 2023

cryo-EM structure of human Aichi virus

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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