|
|
| Line 3: |
Line 3: |
| | <StructureSection load='1m06' size='340' side='right'caption='[[1m06]], [[Resolution|resolution]] 3.50Å' scene=''> | | <StructureSection load='1m06' size='340' side='right'caption='[[1m06]], [[Resolution|resolution]] 3.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1m06]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [https://en.wikipedia.org/wiki/Bpal3 Bpal3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M06 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1m06]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_alpha3 Escherichia phage alpha3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M06 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bpa|2bpa]], [[1cd3|1cd3]], [[1gff|1gff]], [[1phx|1phx]]</div></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=1m06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m06 OCA], [https://pdbe.org/1m06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m06 RCSB], [https://www.ebi.ac.uk/pdbsum/1m06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m06 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=1m06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m06 OCA], [https://pdbe.org/1m06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m06 RCSB], [https://www.ebi.ac.uk/pdbsum/1m06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m06 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/VGF_BPAL3 VGF_BPAL3]] F protein is the major capsid component. [[https://www.uniprot.org/uniprot/VGJ_BPAL3 VGJ_BPAL3]] The J protein is associated with the DNA and is situated in an interior cleft of the F protein (By similarity). [[https://www.uniprot.org/uniprot/G_BPAL3 G_BPAL3]] Attaches the circulating virion to the bacterial lipopolysaccharides which serve as receptor for the virus. Determines the phage host-range. Probably triggers with protein H the injection of the phage DNA into the host cytoplasm upon conformational changes induced by the interaction with host lipopolysaccharides (By similarity).
| + | [https://www.uniprot.org/uniprot/CAPSD_BPAL3 CAPSD_BPAL3] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F. Upon virus binding to host cell, one of the spikes dissociates from the capsid and the virus interacts with LPS through the exposed EF loops on the F proteins. After the genome had been ejected, the channel formed by the F proteins at the unique fivefold axis remains open.[UniProtKB:P03641] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 33: |
Line 32: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpal3]] | + | [[Category: Escherichia phage alpha3]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Baker, T S]] | + | [[Category: Baker TS]] |
| - | [[Category: Bernal, R A]] | + | [[Category: Bernal RA]] |
| - | [[Category: Bowman, V]] | + | [[Category: Bowman V]] |
| - | [[Category: Chipman, P R]] | + | [[Category: Chipman PR]] |
| - | [[Category: Fane, B A]] | + | [[Category: Fane BA]] |
| - | [[Category: Hafenstein, S]] | + | [[Category: Hafenstein S]] |
| - | [[Category: Olson, N H]] | + | [[Category: Olson NH]] |
| - | [[Category: Rossmann, M G]] | + | [[Category: Rossmann MG]] |
| - | [[Category: Assembly]]
| + | |
| - | [[Category: Bacteriophage]]
| + | |
| - | [[Category: Icosahedral virus]]
| + | |
| - | [[Category: Microviridae]]
| + | |
| - | [[Category: Morphogenesis]]
| + | |
| - | [[Category: Phix174]]
| + | |
| - | [[Category: Three-dimensional structure]]
| + | |
| - | [[Category: Virion]]
| + | |
| - | [[Category: Virus-dna complex]]
| + | |
| Structural highlights
Function
CAPSD_BPAL3 Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F. Upon virus binding to host cell, one of the spikes dissociates from the capsid and the virus interacts with LPS through the exposed EF loops on the F proteins. After the genome had been ejected, the channel formed by the F proteins at the unique fivefold axis remains open.[UniProtKB:P03641]
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
Bacteriophage alpha3 is a member of the Microviridae, a family of small, single-stranded, icosahedral phages that include phiX174. These viruses have an ssDNA genome associated with approximately 12 copies of an H pilot protein and 60 copies of a small J DNA-binding protein. The surrounding capsid consists of 60 F coat proteins decorated with 12 pentameric spikes of G protein. Assembly proceeds via a 108S empty procapsid that requires the external D and internal B scaffolding proteins for its formation.The alpha3 "open" procapsid structural intermediate was determined to 15A resolution by cryo-electron microscopy (cryo-EM). Unlike the phiX174 "closed" procapsid and the infectious virion, the alpha3 open procapsid has 30A wide pores at the 3-fold vertices and 20A wide gaps between F pentamers as a result of the disordering of two helices in the F capsid protein. The large pores are probably used for DNA entry and internal scaffolding protein exit during DNA packaging. Portions of the B scaffolding protein are located at the 5-fold axes under the spike and in the hydrophobic pocket on the inner surface of the capsid. Protein B appears to have autoproteolytic activity that cleaves at an Arg-Phe motif and probably facilitates the removal of the protein through the 30A wide pores.The structure of the alpha3 mature virion was solved to 3.5A resolution by X-ray crystallography and was used to interpret the open procapsid cryo-EM structure. The main differences between the alpha3 and phiX174 virion structures are in the spike and the DNA-binding proteins. The alpha3 pentameric spikes have a rotation of 3.5 degrees compared to those of phiX174. The alpha3 DNA-binding protein, which is shorter by 13 amino acid residues at its amino end when compared to the phiX174 J protein, retains its carboxy-terminal-binding site on the internal surface of the capsid protein. The icosahedrally ordered structural component of the ssDNA appears to be substantially increased in alpha3 compared to phiX174, allowing the building of about 10% of the ribose-phosphate backbone.
Structural studies of bacteriophage alpha3 assembly.,Bernal RA, Hafenstein S, Olson NH, Bowman VD, Chipman PR, Baker TS, Fane BA, Rossmann MG J Mol Biol. 2003 Jan 3;325(1):11-24. PMID:12473449[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bernal RA, Hafenstein S, Olson NH, Bowman VD, Chipman PR, Baker TS, Fane BA, Rossmann MG. Structural studies of bacteriophage alpha3 assembly. J Mol Biol. 2003 Jan 3;325(1):11-24. PMID:12473449
|
