2c9g

From Proteopedia

(Difference between revisions)

Current revision

THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON BASE DODECAHEDRON

2c9g, resolution 9.30Å

Structural highlights

2c9g is a 5 chain structure with sequence from Human adenovirus 2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 9.3Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSP_ADE02 Major capsid protein that self-associates to form penton base pentamers, each in the shape of a pentagon, situated at the 12 vertices of the pseudo T=25 capsid. Involved in virus secondary attachment to host cell after initial attachment by the fiber protein. Binds host integrin heterodimer ITGAV-ITGB5 (alphaV-beta5) thereby triggering clathrin-mediated endocytosis of virions. Mediates initial virus attachment to CXADR-negative cells. Binding to integrins ITGAV-ITGB5 also seems to induce macropinocytosis uptake of the virus. As the virus enters the host cell, penton proteins are shed concomitant with virion acidification in the endosome.^[1] ^[2] ^[3]

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

The sub-viral dodecahedral particle of human adenovirus type 3, composed of the viral penton base and fiber proteins, shares an important characteristic of the entire virus: it can attach to cells and penetrate them. Structure determination of the fiberless dodecahedron by cryo-electron microscopy to 9 Angstroms resolution reveals tightly bound pentamer subunits, with only minimal interfaces between penton bases stabilizing the fragile dodecahedron. The internal cavity of the dodecahedron is approximately 80 Angstroms in diameter, and the interior surface is accessible to solvent through perforations of approximately 20 Angstroms diameter between the pentamer towers. We observe weak density beneath pentamers that we attribute to a penton base peptide including residues 38-48. The intact amino-terminal domain appears to interfere with pentamer-pentamer interactions and its absence by mutation or proteolysis is essential for dodecamer assembly. Differences between the 9 Angstroms dodecahedron structure and the adenovirus serotype 2 (Ad2) crystallographic model correlate closely with differences in sequence. The 3D structure of the dodecahedron including fibers at 16 Angstroms resolution reveals extra density on the top of the penton base that can be attributed to the fiber N terminus. The fiber itself exhibits striations that correlate with features of the atomic structure of the partial Ad2 fiber and that represent a repeat motif present in the amino acid sequence. These new observations offer important insights into particle assembly and stability, as well as the practicality of using the dodecahedron in targeted drug delivery. The structural work provides a sound basis for manipulating the properties of this particle and thereby enhancing its value for such therapeutic use.

Structure of the dodecahedral penton particle from human adenovirus type 3.,Fuschiotti P, Schoehn G, Fender P, Fabry CM, Hewat EA, Chroboczek J, Ruigrok RW, Conway JF J Mol Biol. 2006 Feb 17;356(2):510-20. Epub 2005 Dec 9. PMID:16375921^[4]

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

References

↑ Meier O, Boucke K, Hammer SV, Keller S, Stidwill RP, Hemmi S, Greber UF. Adenovirus triggers macropinocytosis and endosomal leakage together with its clathrin-mediated uptake. J Cell Biol. 2002 Sep 16;158(6):1119-31. Epub 2002 Sep 9. PMID:12221069 doi:http://dx.doi.org/10.1083/jcb.200112067
↑ Lyle C, McCormick F. Integrin alphavbeta5 is a primary receptor for adenovirus in CAR-negative cells. Virol J. 2010 Jul 8;7:148. doi: 10.1186/1743-422X-7-148. PMID:20615244 doi:10.1186/1743-422X-7-148
↑ Liu H, Jin L, Koh SB, Atanasov I, Schein S, Wu L, Zhou ZH. Atomic structure of human adenovirus by cryo-EM reveals interactions among protein networks. Science. 2010 Aug 27;329(5995):1038-43. PMID:20798312 doi:10.1126/science.1187433
↑ Fuschiotti P, Schoehn G, Fender P, Fabry CM, Hewat EA, Chroboczek J, Ruigrok RW, Conway JF. Structure of the dodecahedral penton particle from human adenovirus type 3. J Mol Biol. 2006 Feb 17;356(2):510-20. Epub 2005 Dec 9. PMID:16375921 doi:10.1016/j.jmb.2005.11.048

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c9g"

@@ Line 1: / Line 1: @@
 ==THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON BASE DODECAHEDRON==
-<StructureSection load='2c9g' size='340' side='right' caption='[[2c9g]], [[Resolution|resolution]] 9.30&Aring;' scene=''>
+<SX load='2c9g' size='340' side='right' viewer='molstar' caption='[[2c9g]], [[Resolution|resolution]] 9.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c9g]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_adenovirus_2 Human adenovirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C9G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C9G FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c9g]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_adenovirus_2 Human adenovirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C9G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C9G FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x9p|1x9p]], [[1x9t|1x9t]], [[2bld|2bld]], [[2bvi|2bvi]], [[2c6s|2c6s]]</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]] 9.3&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c9g RCSB], [http://www.ebi.ac.uk/pdbsum/2c9g PDBsum]</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=2c9g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c9g OCA], [https://pdbe.org/2c9g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c9g RCSB], [https://www.ebi.ac.uk/pdbsum/2c9g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c9g ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSP_ADE02 CAPSP_ADE02] Major capsid protein that self-associates to form penton base pentamers, each in the shape of a pentagon, situated at the 12 vertices of the pseudo T=25 capsid. Involved in virus secondary attachment to host cell after initial attachment by the fiber protein. Binds host integrin heterodimer ITGAV-ITGB5 (alphaV-beta5) thereby triggering clathrin-mediated endocytosis of virions. Mediates initial virus attachment to CXADR-negative cells. Binding to integrins ITGAV-ITGB5 also seems to induce macropinocytosis uptake of the virus. As the virus enters the host cell, penton proteins are shed concomitant with virion acidification in the endosome.<ref>PMID:12221069</ref> <ref>PMID:20615244</ref> <ref>PMID:20798312</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/c9/2c9g_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c9/2c9g_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=2c9g ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2c9g" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
 [[Category: Human adenovirus 2]]
-[[Category: Chroboczek, J.]]
+[[Category: Large Structures]]
-[[Category: Conway, J F.]]
+[[Category: Chroboczek J]]
-[[Category: Fabry, C M.S.]]
+[[Category: Conway JF]]
-[[Category: Fender, P.]]
+[[Category: Fabry CMS]]
-[[Category: Fuschiotti, P.]]
+[[Category: Fender P]]
-[[Category: Hewat, E A.]]
+[[Category: Fuschiotti P]]
-[[Category: Ruigrok, R W.H.]]
+[[Category: Hewat EA]]
-[[Category: Schoehn, G.]]
+[[Category: Ruigrok RWH]]
-[[Category: Dodecahedron]]
+[[Category: Schoehn G]]
-[[Category: Fibre]]
-[[Category: Late protein]]
-[[Category: Penton]]
-[[Category: Virus-viral protein complex]]

2c9g

From Proteopedia

Current revision

THE QUASI-ATOMIC MODEL OF THE ADENOVIRUS TYPE 3 PENTON BASE DODECAHEDRON

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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