This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2fsy

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Bacteriophage HK97 Pepsin-treated Expansion Intermediate IV

2fsy, resolution 3.80Å

Structural highlights

2fsy 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:	X-ray diffraction, Resolution 3.8Å
Experimental data:	Check to display Experimental Data
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

Checkto colour the structure by Evolutionary Conservation, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Maturation of the bacteriophage HK97 capsid from a precursor (Prohead II) to the mature state (Head II) involves a 60 A radial expansion. The mature particle is formed by 420 copies of the major capsid protein organized on a T = 7 laevo lattice with each subunit covalently crosslinked to two neighbors. Well-characterized pH 4 expansion intermediates make HK97 valuable for investigating quaternary structural dynamics. Here, we use X-ray crystallography and cryo-EM to demonstrate that in the final transition in maturation (requiring neutral pH), pentons in Expansion Intermediate IV (EI-IV) reversibly sample 14 A translations and 6 degrees rotations relative to a fixed hexon lattice. The limit of this trajectory corresponds to the Head II conformation that is secured at this extent only by the formation of the final class of covalent crosslinks. Mutants that cannot crosslink or EI-IV particles that have been rendered incapable of forming the final crosslink remain in the EI-IV state.

Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM.,Gan L, Speir JA, Conway JF, Lander G, Cheng N, Firek BA, Hendrix RW, Duda RL, Liljas L, Johnson JE Structure. 2006 Nov;14(11):1655-65. PMID:17098191^[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
↑ Gan L, Speir JA, Conway JF, Lander G, Cheng N, Firek BA, Hendrix RW, Duda RL, Liljas L, Johnson JE. Capsid conformational sampling in HK97 maturation visualized by X-ray crystallography and cryo-EM. Structure. 2006 Nov;14(11):1655-65. PMID:17098191 doi:10.1016/j.str.2006.09.006

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/2fsy"

@@ Line 1: / Line 1: @@
 ==Bacteriophage HK97 Pepsin-treated Expansion Intermediate IV==
-<StructureSection load='2fsy' size='340' side='right' caption='[[2fsy]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
+<SX load='2fsy' size='340' side='right' viewer='molstar' caption='[[2fsy]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2fsy]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Bphk7 Bphk7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FSY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FSY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fsy]] 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=2FSY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FSY FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2frp|2frp]], [[2fs3|2fs3]], [[2ft1|2ft1]], [[2fte|2fte]]</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]] 3.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">5 ([http://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=2fsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fsy OCA], [https://pdbe.org/2fsy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fsy RCSB], [https://www.ebi.ac.uk/pdbsum/2fsy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fsy ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fsy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fsy OCA], [http://pdbe.org/2fsy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fsy RCSB], [http://www.ebi.ac.uk/pdbsum/2fsy PDBsum]</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]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fs/2fsy_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fs/2fsy_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2fsy ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 31: @@
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Bphk7]]
+[[Category: Escherichia virus HK97]]
-[[Category: Cheng, N]]
+[[Category: Large Structures]]
-[[Category: Conway, J F]]
+[[Category: Cheng N]]
-[[Category: Duda, R L]]
+[[Category: Conway JF]]
-[[Category: Firek, B A]]
+[[Category: Duda RL]]
-[[Category: Gan, L]]
+[[Category: Firek BA]]
-[[Category: Hendrix, R W]]
+[[Category: Gan L]]
-[[Category: Johnson, J E]]
+[[Category: Hendrix RW]]
-[[Category: Lander, G]]
+[[Category: Johnson JE]]
-[[Category: Liljas, L]]
+[[Category: Lander G]]
-[[Category: Speir, J A]]
+[[Category: Liljas L]]
-[[Category: Bacteriophage]]
+[[Category: Speir JA]]
-[[Category: Capsid protein]]
-[[Category: Expansion intermediate]]
-[[Category: Hk97]]
-[[Category: Icosahedral virus]]
-[[Category: Virus]]

2fsy

From Proteopedia

Current revision

Bacteriophage HK97 Pepsin-treated Expansion Intermediate IV

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox