5aoo

From Proteopedia

(Difference between revisions)

Revision as of 06:20, 31 May 2023

X-ray structure of a human Kobuvirus: Aichi virus A (AiV)

Structural highlights

5aoo is a 3 chain structure with sequence from Aichivirus A. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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

Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of the domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 A resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 A r.m.s.d. for C(alpha) atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.

The use of noncrystallographic symmetry averaging to solve structures from data affected by perfect hemihedral twinning.,Sabin C, Plevka P Acta Crystallogr F Struct Biol Commun. 2016 Mar 1;72(Pt 3):188-97. doi:, 10.1107/S2053230X16000923. Epub 2016 Feb 16. PMID:26919522^[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
↑ Sabin C, Plevka P. The use of noncrystallographic symmetry averaging to solve structures from data affected by perfect hemihedral twinning. Acta Crystallogr F Struct Biol Commun. 2016 Mar 1;72(Pt 3):188-97. doi:, 10.1107/S2053230X16000923. Epub 2016 Feb 16. PMID:26919522 doi:http://dx.doi.org/10.1107/S2053230X16000923

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/5aoo"

Categories: Aichivirus A | Large Structures | Palkova L | Plevka P | Sabin C

@@ Line 3: / Line 3: @@
 <StructureSection load='5aoo' size='340' side='right'caption='[[5aoo]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5aoo]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Aichivirus_a Aichivirus a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AOO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AOO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5aoo]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aichivirus_A Aichivirus A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AOO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AOO FirstGlance]. <br>
-</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=5aoo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aoo OCA], [http://pdbe.org/5aoo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5aoo RCSB], [http://www.ebi.ac.uk/pdbsum/5aoo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5aoo ProSAT]</span></td></tr>
+</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=5aoo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5aoo OCA], [https://pdbe.org/5aoo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5aoo RCSB], [https://www.ebi.ac.uk/pdbsum/5aoo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5aoo 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 21: @@
 __TOC__
 </StructureSection>
-[[Category: Aichivirus a]]
+[[Category: Aichivirus A]]
 [[Category: Large Structures]]
-[[Category: Palkova, L]]
+[[Category: Palkova L]]
-[[Category: Plevka, P]]
+[[Category: Plevka P]]
-[[Category: Sabin, C]]
+[[Category: Sabin C]]
-[[Category: Acute gastroenterisis]]
-[[Category: Aichi virus]]
-[[Category: Full virus particle]]
-[[Category: Icosahedral capsid]]
-[[Category: Kobuvirus]]
-[[Category: Picornavirus]]
-[[Category: Virus]]

5aoo

From Proteopedia

Revision as of 06:20, 31 May 2023

X-ray structure of a human Kobuvirus: Aichi virus A (AiV)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox