2ifm: Difference between revisions

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<StructureSection load='2ifm' size='340' side='right'caption='[[2ifm]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
<StructureSection load='2ifm' size='340' side='right'caption='[[2ifm]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2ifm]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xanthomonas_phage_xf Xanthomonas phage xf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IFM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2IFM FirstGlance]. <br>
<table><tr><td colspan='2'>[[2ifm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_phage_Xf Xanthomonas phage Xf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IFM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IFM FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ifd|1ifd]], [[1ifm|1ifm]], [[3ifm|3ifm]], [[4ifm|4ifm]], [[1ifi|1ifi]], [[1ifj|1ifj]], [[1ifk|1ifk]], [[1ifl|1ifl]], [[1ifn|1ifn]], [[2ifo|2ifo]]</td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Fiber diffraction, [[Resolution|Resolution]] 3.3&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ifm OCA], [http://pdbe.org/2ifm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ifm RCSB], [http://www.ebi.ac.uk/pdbsum/2ifm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ifm 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=2ifm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ifm OCA], [https://pdbe.org/2ifm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ifm RCSB], [https://www.ebi.ac.uk/pdbsum/2ifm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ifm ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/CAPSD_BPPF1 CAPSD_BPPF1]] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).  
[https://www.uniprot.org/uniprot/CAPSD_BPPF1 CAPSD_BPPF1] Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The filamentous bacteriophage Pf1 is structurally similar to the well known Ff (fd, fl, M13) strains, but it gives much better X-ray diffraction patterns, enabling a more detailed analysis of the molecular structure. The 46-residue protein subunit can be closely approximated by a single gently curved stretch of alpha-helix. The axes of the subunits are at a small angle to the virion axis, and several thousand subunits form an overlapping inter-digitated helical array surrounding a DNA core. We have derived a detailed model of the virion based on X-ray data and stereochemical constraints. We have considered potential sources of error in the diffraction data, and used the improved data to study regions where the protein subunit of Pf1 may deviate from a continuous alpha-helix. We use simulated annealing to escape from local minima, and various kinds of electron-density maps to guide the model building. Refinement of the model shows that the first few residues at the N terminus are non-helical, and there is a slight discontinuity in the alpha-helix near the middle of the sequence. The model is consistent both with general structural principles derived from high-resolution analysis of other proteins, and with specific chemical and spectroscopic data about Pf1. We apply the same refinement techniques to an alternative model with a non-helical surface loop between residues 13 and 19. Comparative analysis of models with and without a loop shows that the loop model is not supported by 3.3 A resolution X-ray diffraction data.
 
Pf1 filamentous bacteriophage: refinement of a molecular model by simulated annealing using 3.3 A resolution X-ray fibre diffraction data.,Gonzalez A, Nave C, Marvin DA Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):792-804. PMID:15299811<ref>PMID:15299811</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2ifm" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[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: Large Structures]]
[[Category: Large Structures]]
[[Category: Xanthomonas phage xf]]
[[Category: Xanthomonas phage Xf]]
[[Category: Marvin, D A]]
[[Category: Marvin DA]]
[[Category: Helical virus]]
[[Category: Virus]]
[[Category: Virus coat protein]]

Latest revision as of 12:02, 21 February 2024

PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATAPF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA

Structural highlights

2ifm is a 1 chain structure with sequence from Xanthomonas phage Xf. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Fiber diffraction, Resolution 3.3Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BPPF1 Self assembles to form a helical capsid wrapping up the viral genomic DNA. The capsid displays a filamentous structure with a length of 760-1950 nm and a width of 6-8 nm. The virion assembly and budding take place at the host inner membrane (By similarity).

See Also

2ifm, resolution 3.30Å

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