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.

5gai

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:45, 18 July 2018

Warning: this is a large structure, and loading might take a long time or not happen at all.

Probabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike proteins

Structural highlights

5gai is a 27 chain structure with sequence from Bpp22. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Warning: this is a large structure, and loading might take a long time or not happen at all.

Function

[PORTL_BPP22] Required for successful condensation of DNA within the capsid. Gp1 is a minor structural protein. The portal protein is present as a single ring-shaped dodecamer located at the point where tails attach. It is through this ring that DNA is thought to enter the prohead. [FIBER_BPP22] Structural component of the short non-contractile tail. The tail comprises six fibers that mediate primary attachment to the host cell lipopolysaccharides (LPS) and display endorhamnosidase enzymatic activity, hydrolyzing the alpha-1,3-O-glycosidic linkage between rhamnose and galactose of the O-antigen polysaccharide. Digestion of the LPS brings the capsid near the cell outer membrane.^[1] ^[2] [EXLYS_BPP22] Tail protein located at the vertex occupied by the portal ring. Together with gp10 and gp26, gp4 is required for stabilization of the condensed DNA within the capsid; perhaps by plugging the hole through which the DNA enters. Plays a role in ejection of the bacteriophage DNA into the host cell at the initiation of infection. Functions as an exolysin that catalyzes the cleavage of the glycosidic bonds between N-acetylmuramic acid and N-acetylglucosamine residues in peptidoglycans.^[3]

Publication Abstract from PubMed

CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions, which can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 A), whereas other components are at slightly lower resolutions: portal (9.2 A), hub (8.5 A), tailspike (10.9 A), and needle (10.5 A). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density.

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.,Pintilie G, Chen DH, Haase-Pettingell CA, King JA, Chiu W Biophys J. 2016 Feb 23;110(4):827-39. doi: 10.1016/j.bpj.2015.11.3522. Epub 2015 , Dec 30. PMID:26743049^[4]

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

References

↑ Weigele PR, Scanlon E, King J. Homotrimeric, beta-stranded viral adhesins and tail proteins. J Bacteriol. 2003 Jul;185(14):4022-30. PMID:12837775
↑ Andres D, Hanke C, Baxa U, Seul A, Barbirz S, Seckler R. Tailspike interactions with lipopolysaccharide effect DNA ejection from phage P22 particles in vitro. J Biol Chem. 2010 Nov 19;285(47):36768-75. doi: 10.1074/jbc.M110.169003. Epub, 2010 Sep 3. PMID:20817910 doi:http://dx.doi.org/10.1074/jbc.M110.169003
↑ Moak M, Molineux IJ. Peptidoglycan hydrolytic activities associated with bacteriophage virions. Mol Microbiol. 2004 Feb;51(4):1169-83. PMID:14763988
↑ Pintilie G, Chen DH, Haase-Pettingell CA, King JA, Chiu W. Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage. Biophys J. 2016 Feb 23;110(4):827-39. doi: 10.1016/j.bpj.2015.11.3522. Epub 2015 , Dec 30. PMID:26743049 doi:http://dx.doi.org/10.1016/j.bpj.2015.11.3522

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5gai"

@@ Line 3: / Line 3: @@
 <StructureSection load='5gai' size='340' side='right' caption='[[5gai]], [[Resolution|resolution]] 10.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gai]] is a 27 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GAI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gai]] is a 27 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpp22 Bpp22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GAI FirstGlance]. <br>
 </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=5gai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gai OCA], [http://pdbe.org/5gai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gai RCSB], [http://www.ebi.ac.uk/pdbsum/5gai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gai ProSAT]</span></td></tr>
 </table>
@@ Line 18: / Line 18: @@
 </div>
 <div class="pdbe-citations 5gai" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Portal protein|Portal protein]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Bpp22]]
 [[Category: Chen, D H]]
 [[Category: Chiu, W]]

5gai

From Proteopedia

Revision as of 08:45, 18 July 2018

Probabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike proteins

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox