3ddx: Difference between revisions

Latest revision as of 08:27, 5 March 2025

HK97 bacteriophage capsid Expansion Intermediate-II model

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Structural highlights

3ddx is a 7 chain structure with sequence from Escherichia virus HK97. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 14Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BPHK7 Assembles to form an icosahedral capsid of 66 nm, with a T=7 laevo symmetry (PubMed:11000116, PubMed:21276801). Responsible for its self-assembly into a procapsid. The phage does not need to encode a separate scaffolfing protein because its capsid protein contains the delta domain that carries that function.^[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

The capsids of tailed-DNA bacteriophages first assemble as procapsids, which mature by converting into a new form that is strong enough to contain a densely packed viral chromosome. We demonstrate that the intersubunit crosslinking that occurs during maturation of HK97 capsids actually promotes the structural transformation. Small-angle X-ray scattering and crosslinking assays reveal that a shift in the crosslink pattern accompanies conversion of a semimature particle, Expansion Intermediate-I/II, to a more mature state, Balloon. This transition occurs in a switch-like fashion. We find that crosslink formation shifts the global conformational balance to favor the balloon state. A pseudoatomic model of EI-I/II derived from cryo-EM provides insight into the relationship between crosslink formation and conformational switching.

Virus capsid expansion driven by the capture of mobile surface loops.,Lee KK, Gan L, Tsuruta H, Moyer C, Conway JF, Duda RL, Hendrix RW, Steven AC, Johnson JE Structure. 2008 Oct 8;16(10):1491-502. PMID:18940605^[5]

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

References

↑ Wikoff WR, Liljas L, Duda RL, Tsuruta H, Hendrix RW, Johnson JE. Topologically linked protein rings in the bacteriophage HK97 capsid. Science. 2000 Sep 22;289(5487):2129-33. PMID:11000116
↑ Huang RK, Khayat R, Lee KK, Gertsman I, Duda RL, Hendrix RW, Johnson JE. The Prohead-I Structure of Bacteriophage HK97: Implications for Scaffold-Mediated Control of Particle Assembly and Maturation. J Mol Biol. 2011 Jan 27. PMID:21276801 doi:10.1016/j.jmb.2011.01.016
↑ Duda RL, Martincic K, Xie Z, Hendrix RW. Bacteriophage HK97 head assembly. FEMS Microbiol Rev. 1995 Aug;17(1-2):41-6. PMID:7669350 doi:10.1111/j.1574-6976.1995.tb00186.x
↑ Duda RL, Martincic K, Hendrix RW. Genetic basis of bacteriophage HK97 prohead assembly. J Mol Biol. 1995 Apr 7;247(4):636-47. PMID:7723020 doi:10.1006/jmbi.1994.0169
↑ Lee KK, Gan L, Tsuruta H, Moyer C, Conway JF, Duda RL, Hendrix RW, Steven AC, Johnson JE. Virus capsid expansion driven by the capture of mobile surface loops. Structure. 2008 Oct 8;16(10):1491-502. PMID:18940605 doi:https://dx.doi.org/10.1016/j.str.2008.06.014

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Wikoff WR, Liljas L, Duda RL, Tsuruta H, Hendrix RW, Johnson JE. Topologically linked protein rings in the bacteriophage HK97 capsid. Science. 2000 Sep 22;289(5487):2129-33. PMID:11000116

[2] Huang RK, Khayat R, Lee KK, Gertsman I, Duda RL, Hendrix RW, Johnson JE. The Prohead-I Structure of Bacteriophage HK97: Implications for Scaffold-Mediated Control of Particle Assembly and Maturation. J Mol Biol. 2011 Jan 27. PMID:21276801 doi:10.1016/j.jmb.2011.01.016

[3] Duda RL, Martincic K, Xie Z, Hendrix RW. Bacteriophage HK97 head assembly. FEMS Microbiol Rev. 1995 Aug;17(1-2):41-6. PMID:7669350 doi:10.1111/j.1574-6976.1995.tb00186.x

[4] Duda RL, Martincic K, Hendrix RW. Genetic basis of bacteriophage HK97 prohead assembly. J Mol Biol. 1995 Apr 7;247(4):636-47. PMID:7723020 doi:10.1006/jmbi.1994.0169

[5] Lee KK, Gan L, Tsuruta H, Moyer C, Conway JF, Duda RL, Hendrix RW, Steven AC, Johnson JE. Virus capsid expansion driven by the capture of mobile surface loops. Structure. 2008 Oct 8;16(10):1491-502. PMID:18940605 doi:https://dx.doi.org/10.1016/j.str.2008.06.014

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[2]

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[5]

@@ Line 1: / Line 1: @@
 ==HK97 bacteriophage capsid Expansion Intermediate-II model==
-<SX load='3ddx' size='340' side='right' viewer='molstar' caption='[[3ddx]]' scene=''>
+<SX load='3ddx' size='340' side='right' viewer='molstar' caption='[[3ddx]], [[Resolution|resolution]] 14.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ddx]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Bphk7 Bphk7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ddx]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_HK97 Escherichia virus HK97]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DDX FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fte|2fte]], [[1ohg|1ohg]], [[2gp1|2gp1]]</div></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 14&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=37554 BPHK7])</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=3ddx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ddx OCA], [https://pdbe.org/3ddx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ddx RCSB], [https://www.ebi.ac.uk/pdbsum/3ddx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ddx ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSD_BPHK7 CAPSD_BPHK7] Assembles to form an icosahedral capsid of 66 nm, with a T=7 laevo symmetry (PubMed:11000116, PubMed:21276801). Responsible for its self-assembly into a procapsid. The phage does not need to encode a separate scaffolfing protein because its capsid protein contains the delta domain that carries that function.<ref>PMID:11000116</ref> <ref>PMID:21276801</ref> <ref>PMID:7669350</ref> <ref>PMID:7723020</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 13: / Line 14: @@
    <jmolCheckbox>
      <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/3ddx_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 31: / Line 32: @@
 __TOC__
 </SX>
-[[Category: Bphk7]]
+[[Category: Escherichia virus HK97]]
 [[Category: Large Structures]]
-[[Category: Conway, J F]]
+[[Category: Conway JF]]
-[[Category: Gan, L]]
+[[Category: Gan L]]
-[[Category: Hendrix, R W]]
+[[Category: Hendrix RW]]
-[[Category: Johnson, J E]]
+[[Category: Johnson JE]]
-[[Category: Lee, K K]]
+[[Category: Lee KK]]
-[[Category: Steven, A C]]
+[[Category: Steven AC]]
-[[Category: Bacteriophage]]
-[[Category: Capsid protein]]
-[[Category: Expansion intermediate]]
-[[Category: Hk97]]
-[[Category: Icosahedral virus]]
-[[Category: Virion]]
-[[Category: Virus]]

3ddx: Difference between revisions

Latest revision as of 08:27, 5 March 2025

HK97 bacteriophage capsid Expansion Intermediate-II model

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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