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.

3iyx

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 17:31, 10 April 2020

Coordinates of the b1b bridge-forming protein structures fitted into the Cryo-EM map of E.coli 70S ribosome (EMD-1056)

3iyx, resolution 9.00Å

Structural highlights

3iyx is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	2i2p, 2i2t, 2wrj
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[D3QTD7_ECOCB] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity).[HAMAP-Rule:MF_01315] [D3QYD6_ECOCB] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501][SAAS:SAAS027491_004_000769] [D3QTE7_ECOCB] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs (By similarity).[HAMAP-Rule:MF_01333]

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 ribosomal intersubunit bridges maintain the overall architecture of the ribosome and thereby play a pivotal role in the dynamics of translation. The only protein-protein bridge, b1b, is formed by the two proteins, S13 and L5 of the small and large ribosomal subunits, respectively. B1b absorbs the largest movement during ratchet-like motion, and its two proteins reorganize in different constellations during this motion of the ribosome. Our results in this study of b1b in the Escherichia coli 70S ribosome suggest that the intrinsic molecular features of the bridging proteins allow the bridge to modulate the ratchet-like motion in a controlled manner. Additionally, another large subunit protein, L31, seems to participate with S13 and L5 in the formation, dynamics, and stabilization of this bridge.

Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome.,Shasmal M, Chakraborty B, Sengupta J Biochem Biophys Res Commun. 2010 Aug 20;399(2):192-197. Epub 2010 Jul 17. PMID:20643101^[1]

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

References

↑ Shasmal M, Chakraborty B, Sengupta J. Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome. Biochem Biophys Res Commun. 2010 Aug 20;399(2):192-197. Epub 2010 Jul 17. PMID:20643101 doi:10.1016/j.bbrc.2010.07.053

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/3iyx"

@@ Line 3: / Line 3: @@
 <SX load='3iyx' size='340' side='right' viewer='molstar' caption='[[3iyx]], [[Resolution|resolution]] 9.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3iyx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3iyx]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3IYX FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2i2p|2i2p]], [[2i2t|2i2t]], [[2wrj|2wrj]]</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=3iyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyx OCA], [http://pdbe.org/3iyx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iyx RCSB], [http://www.ebi.ac.uk/pdbsum/3iyx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyx ProSAT]</span></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=3iyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyx OCA], [http://pdbe.org/3iyx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iyx RCSB], [http://www.ebi.ac.uk/pdbsum/3iyx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyx ProSAT]</span></td></tr>
 </table>
 == Function ==

3iyx

From Proteopedia

Revision as of 17:31, 10 April 2020

Coordinates of the b1b bridge-forming protein structures fitted into the Cryo-EM map of E.coli 70S ribosome (EMD-1056)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox