1cd3

From Proteopedia

(Difference between revisions)

Revision as of 07:00, 10 October 2019

PROCAPSID OF BACTERIOPHAGE PHIX174

Structural highlights

1cd3 is a 7 chain structure with sequence from Enterobacteria phage 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.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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. [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.^[1] ^[2] [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.^[3] ^[4] [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.^[5]

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^[6]

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

References

↑ Mukai R, Hamatake RK, Hayashi M. Isolation and identification of bacteriophage phi X174 prohead. Proc Natl Acad Sci U S A. 1979 Oct;76(10):4877-81. PMID:159449
↑ Uchiyama A, Fane BA. Identification of an interacting coat-external scaffolding protein domain required for both the initiation of phiX174 procapsid morphogenesis and the completion of DNA packaging. J Virol. 2005 Jun;79(11):6751-6. PMID:15890913 doi:http://dx.doi.org/10.1128/JVI.79.11.6751-6756.2005
↑ Inagaki M, Tanaka A, Suzuki R, Wakashima H, Kawaura T, Karita S, Nishikawa S, Kashimura N. Characterization of the binding of spike H protein of bacteriophage phiX174 with receptor lipopolysaccharides. J Biochem. 2000 Apr;127(4):577-83. PMID:10739948
↑ Inagaki M, Kawaura T, Wakashima H, Kato M, Nishikawa S, Kashimura N. Different contributions of the outer and inner R-core residues of lipopolysaccharide to the recognition by spike H and G proteins of bacteriophage phiX174. FEMS Microbiol Lett. 2003 Sep 26;226(2):221-7. PMID:14553915
↑ 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
↑ 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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1cd3"

@@ Line 1: / Line 1: @@
 ==PROCAPSID OF BACTERIOPHAGE PHIX174==
-<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 ==
 <table><tr><td colspan='2'>[[1cd3]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_phix174 Enterobacteria phage phix174]. The February 2000 RCSB PDB [http://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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CD3 FirstGlance]. <br>
@@ Line 12: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/1cd3_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cd/1cd3_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 [[Category: Bacteriophage phiX174]]
 [[Category: Enterobacteria phage phix174]]
+[[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Dokland, T]]

1cd3

From Proteopedia

Revision as of 07:00, 10 October 2019

PROCAPSID OF BACTERIOPHAGE PHIX174

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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