1cd3: Difference between revisions

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<StructureSection load='1cd3' size='340' side='right'caption='[[1cd3]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
<StructureSection load='1cd3' size='340' side='right'caption='[[1cd3]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1cd3]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_phix174 Enterobacteria phage phix174]. The February 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriophage phiX174''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_2 10.2210/rcsb_pdb/mom_2000_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CD3 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1cd3]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_phiX174 Escherichia virus phiX174]. The February 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriophage phiX174''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_2 10.2210/rcsb_pdb/mom_2000_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CD3 FirstGlance]. <br>
</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=1cd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cd3 OCA], [https://pdbe.org/1cd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1cd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cd3 ProSAT]</span></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]] 3.5&#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=1cd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cd3 OCA], [https://pdbe.org/1cd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1cd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cd3 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/B_BPPHX B_BPPHX]] Participates in the assembly of the viral procapsid in the cytoplasm. Forms first a 12S pre-assembly complex with protein H, and F and G pentamers, then twelve 12S complexes are joined by the D protein to form the procapsid. Internal scaffold protein B is released from the procapsid upon genome packaging, possibly through affinity displacement by the protein J, or by proteolysis. [[https://www.uniprot.org/uniprot/D_BPPHX D_BPPHX]] Assembles the procapsid by joining twelve 12S pre-assembly complex into a T=1 icosahedral particle, called 108S procapsid. Ten proteins D bind each 12S complex, which are formed by three pentamers of F, G, B protein and a H protein. The scaffolding protein is released from the provirion after genome packaging to form the mature virion.<ref>PMID:159449</ref> <ref>PMID:15890913</ref>  [[https://www.uniprot.org/uniprot/G_BPPHX G_BPPHX]] 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.<ref>PMID:10739948</ref> <ref>PMID:14553915</ref> [[https://www.uniprot.org/uniprot/F_BPPHX F_BPPHX]] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F.<ref>PMID:11991963</ref>
[https://www.uniprot.org/uniprot/CAPSD_BPPHS CAPSD_BPPHS] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F (PubMed:11991963, PubMed:1370343, PubMed:8158636). 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 (PubMed:29229840). After the genome had been ejected, the channel formed by the F proteins at the unique fivefold axis remains open (PubMed:29229840).<ref>PMID:11991963</ref> <ref>PMID:1370343</ref> <ref>PMID:29229840</ref> <ref>PMID:8158636</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</StructureSection>
</StructureSection>
[[Category: Bacteriophage phiX174]]
[[Category: Bacteriophage phiX174]]
[[Category: Enterobacteria phage phix174]]
[[Category: Escherichia virus phiX174]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Dokland, T]]
[[Category: Dokland T]]
[[Category: Rossmann, M G]]
[[Category: Rossmann MG]]
[[Category: Bacteriophage]]
[[Category: Chaperone]]
[[Category: Icosahedral virus]]
[[Category: Procapsid]]
[[Category: Scaffolding protein]]
[[Category: Virus]]

Revision as of 02:25, 28 December 2023

PROCAPSID OF BACTERIOPHAGE PHIX174PROCAPSID OF BACTERIOPHAGE PHIX174

Structural highlights

1cd3 is a 7 chain structure with sequence from Escherichia virus phiX174. The February 2000 RCSB PDB Molecule of the Month feature on Bacteriophage phiX174 by David S. Goodsell is 10.2210/rcsb_pdb/mom_2000_2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.5Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BPPHS Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F (PubMed:11991963, PubMed:1370343, PubMed:8158636). 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 (PubMed:29229840). After the genome had been ejected, the channel formed by the F proteins at the unique fivefold axis remains open (PubMed:29229840).[1] [2] [3] [4]

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

An empty precursor particle called the procapsid is formed during assembly of the single-stranded DNA bacteriophage phiX174. Assembly of the phiX174 procapsid requires the presence of the two scaffolding proteins, D and B, which are structural components of the procapsid, but are not found in the mature virion. The X-ray crystallographic structure of a "closed" procapsid particle has been determined to 3.5 A resolution. This structure has an external scaffold made from 240 copies of protein D, 60 copies of the internally located B protein, and contains 60 copies of each of the viral structural proteins F and G, which comprise the shell and the 5-fold spikes, respectively. The F capsid protein has a similar conformation to that seen in the mature virion, and differs from the previously determined 25 A resolution electron microscopic reconstruction of the "open" procapsid, in which the F protein has a different conformation. The D scaffolding protein has a predominantly alpha-helical fold and displays remarkable conformational variability. We report here an improved and refined structure of the closed procapsid and describe in some detail the differences between the four independent D scaffolding proteins per icosahedral asymmetric unit, as well as their interaction with the F capsid protein. We re-analyze and correct the comparison of the closed procapsid with the previously determined cryo-electron microscopic image reconstruction of the open procapsid and discuss the major structural rearrangements that must occur during assembly. A model is proposed in which the D proteins direct the assembly process by sequential binding and conformational switching.

The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174.,Dokland T, Bernal RA, Burch A, Pletnev S, Fane BA, Rossmann MG J Mol Biol. 1999 May 14;288(4):595-608. PMID:10329166[5]

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

References

  1. ↑ Hafenstein S, Fane BA. phi X174 genome-capsid interactions influence the biophysical properties of the virion: evidence for a scaffolding-like function for the genome during the final stages of morphogenesis. J Virol. 2002 Jun;76(11):5350-6. PMID:11991963
  2. ↑ McKenna R, Xia D, Willingmann P, Ilag LL, Krishnaswamy S, Rossmann MG, Olson NH, Baker TS, Incardona NL. Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications. Nature. 1992 Jan 9;355(6356):137-43. PMID:1370343 doi:http://dx.doi.org/10.1038/355137a0
  3. ↑ Sun Y, Roznowski AP, Tokuda JM, Klose T, Mauney A, Pollack L, Fane BA, Rossmann MG. Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):13708-13713. PMID:29229840 doi:10.1073/pnas.1716614114
  4. ↑ McKenna R, Ilag LL, Rossmann MG. Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A. J Mol Biol. 1994 Apr 15;237(5):517-43. PMID:8158636 doi:10.1006/jmbi.1994.1253
  5. ↑ Dokland T, Bernal RA, Burch A, Pletnev S, Fane BA, Rossmann MG. The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174. J Mol Biol. 1999 May 14;288(4):595-608. PMID:10329166 doi:10.1006/jmbi.1999.2699

1cd3, resolution 3.50Å

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