2bbv: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2bbv]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Black_beetle_virus Black beetle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BBV FirstGlance]. <br>
<table><tr><td colspan='2'>[[2bbv]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Black_beetle_virus Black beetle virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BBV FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=2bbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bbv OCA], [https://pdbe.org/2bbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bbv RCSB], [https://www.ebi.ac.uk/pdbsum/2bbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bbv ProSAT]</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=2bbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bbv OCA], [https://pdbe.org/2bbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bbv RCSB], [https://www.ebi.ac.uk/pdbsum/2bbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bbv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/CAPSD_BBV CAPSD_BBV]] Capsid protein alpha self-assembles to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins trimers. In addition, calcium ions are incorporated per capsid during assembly. The capsid encapsulates the two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid protein alpha generating capsid protein beta and the membrane-active peptide gamma (By similarity).  Peptide gamma is a membrane-disrupting peptide produced by virus maturation, thereby creating the infectious virion. After penetration into the host cell, peptide gamma is probably exposed/released in endosomes, where it disrupts the endosomal membrane, facilitating translocation of viral RNA into the cytoplasm (By similarity).  
[https://www.uniprot.org/uniprot/CAPSD_BBV CAPSD_BBV] Capsid protein alpha self-assembles to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins trimers. In addition, calcium ions are incorporated per capsid during assembly. The capsid encapsulates the two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid protein alpha generating capsid protein beta and the membrane-active peptide gamma (By similarity).  Peptide gamma is a membrane-disrupting peptide produced by virus maturation, thereby creating the infectious virion. After penetration into the host cell, peptide gamma is probably exposed/released in endosomes, where it disrupts the endosomal membrane, facilitating translocation of viral RNA into the cytoplasm (By similarity).
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=2bbv 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=2bbv ConSurf].
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<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structure of the black beetle nodavirus has been refined at 2.8 A resolution by alternate use of restrained least-squares atomic coordinate refinement and phase refinement by real space averaging with the 5-fold non-crystallographic symmetry in the crystal. The coordinates were also refined by simulated annealing. The final R-factor for all data with I/sigma(I) &gt; 4 was 22.1%. A total of 7692 atoms were refined in one icosahedral asymmetric unit which included 273 oxygen atoms of ordered water molecules. Three identical gene products of 407 amino acids form one icosahedral asymmetric unit. Each is located in a structurally unique position, identified as A, B or C, consistent with a T = 3 quasi equivalent lattice. Icosahedral pentamers are formed by A subunits while B and C subunits alternate about icosahedral 3-fold axes to form quasi hexamers. Five calcium ions are located within the icosahedral asymmetric unit and stabilize the quasi 3-fold related intersubunit contacts between A, B and C. The final model consists of coordinates for residues 56 to 379 of all three subunits and residues 20 to 31 from the C subunit only. Atom positions for the sugar-phosphate backbone were modeled for ten nucleotides close to the icosahedral 2-fold axes. Symmetry equivalent polyribonucleotides form a helical duplex at each icosahedral 2-fold axis. The three subunits display an eight-stranded beta-barrel fold, very similar to the subunit structures observed in most other icosahedral RNA viruses analyzed. Quasi equivalence is regulated by the ordered RNA and residues 20 to 31 in the C subunit to form a "flat inter subunit contact" at icosahedral 2-fold joints. The RNA and polypeptide are disordered at the quasi 2-fold joints and this results in a "bent inter subunit contact". Although similar quaternary structures were seen in T = 3 plant viruses studied, RNA did not play a role as a molecular switch in those structures. The autocatalytic, post assembly, cleavage of the initial gene product at residue Asn363/Ala364 to form a stable and infectious particle is probably the result of an acid catalyzed main-chain hydrolysis in which Asp75 is the proton donor. The reaction is initiated by assembly which places Asp75 in a hydrophobic environment created by quaternary interactions which raises its pK to 5.6. The region in which the reaction occurs is formed by an internal helical bundle that has not been seen in other virus structures.
The refined three-dimensional structure of an insect virus at 2.8 A resolution.,Wery JP, Reddy VS, Hosur MV, Johnson JE J Mol Biol. 1994 Jan 14;235(2):565-86. PMID:8289282<ref>PMID:8289282</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2bbv" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Black beetle virus]]
[[Category: Black beetle virus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Hosur, M V]]
[[Category: Hosur MV]]
[[Category: Johnson, J E]]
[[Category: Johnson JE]]
[[Category: Reddy, V S]]
[[Category: Reddy VS]]
[[Category: Wery, J P]]
[[Category: Wery J-P]]
[[Category: Double helix]]
[[Category: Icosahedral virus]]
[[Category: Protein-rna complex]]
[[Category: Virus-rna complex]]

Latest revision as of 12:16, 14 February 2024

THE REFINED THREE-DIMENSIONAL STRUCTURE OF AN INSECT VIRUS AT 2.8 ANGSTROMS RESOLUTIONTHE REFINED THREE-DIMENSIONAL STRUCTURE OF AN INSECT VIRUS AT 2.8 ANGSTROMS RESOLUTION

Structural highlights

2bbv is a 7 chain structure with sequence from Black beetle virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BBV Capsid protein alpha self-assembles to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins trimers. In addition, calcium ions are incorporated per capsid during assembly. The capsid encapsulates the two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid protein alpha generating capsid protein beta and the membrane-active peptide gamma (By similarity). Peptide gamma is a membrane-disrupting peptide produced by virus maturation, thereby creating the infectious virion. After penetration into the host cell, peptide gamma is probably exposed/released in endosomes, where it disrupts the endosomal membrane, facilitating translocation of viral RNA into the cytoplasm (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

2bbv, resolution 2.80Å

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