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.

2o0f

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Docking of the modified RF3 X-ray structure into cryo-EM map of E.coli 70S ribosome bound with RF3

2o0f, resolution 15.50Å

Structural highlights

2o0f is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 15.5Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RF3_ECOLI Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP.[HAMAP-Rule:MF_00072]

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

During translation termination, class II release factor RF3 binds to the ribosome to promote rapid dissociation of a class I release factor (RF) in a GTP-dependent manner. We present the crystal structure of E. coli RF3*GDP, which has a three-domain architecture strikingly similar to the structure of EF-Tu*GTP. Biochemical data on RF3 mutants show that a surface region involving domains II and III is important for distinct steps in the action cycle of RF3. Furthermore, we present a cryo-electron microscopy (cryo-EM) structure of the posttermination ribosome bound with RF3 in the GTP form. Our data show that RF3*GTP binding induces large conformational changes in the ribosome, which break the interactions of the class I RF with both the decoding center and the GTPase-associated center of the ribosome, apparently leading to the release of the class I RF.

RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors.,Gao H, Zhou Z, Rawat U, Huang C, Bouakaz L, Wang C, Cheng Z, Liu Y, Zavialov A, Gursky R, Sanyal S, Ehrenberg M, Frank J, Song H Cell. 2007 Jun 1;129(5):929-41. PMID:17540173^[1]

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

References

↑ Gao H, Zhou Z, Rawat U, Huang C, Bouakaz L, Wang C, Cheng Z, Liu Y, Zavialov A, Gursky R, Sanyal S, Ehrenberg M, Frank J, Song H. RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell. 2007 Jun 1;129(5):929-41. PMID:17540173 doi:10.1016/j.cell.2007.03.050

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/2o0f"

@@ Line 3: / Line 3: @@
 <SX load='2o0f' size='340' side='right' viewer='molstar' caption='[[2o0f]], [[Resolution|resolution]] 15.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2o0f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O0F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2o0f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O0F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O0F 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;'>[[2h5e|2h5e]]</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]] 15.5&#8491;</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=2o0f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o0f OCA], [https://pdbe.org/2o0f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o0f RCSB], [https://www.ebi.ac.uk/pdbsum/2o0f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o0f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/Q0T8T9_ECOL5 Q0T8T9_ECOL5]] Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP (By similarity).[HAMAP-Rule:MF_00072][SAAS:SAAS004548_004_056011]
+[https://www.uniprot.org/uniprot/RF3_ECOLI RF3_ECOLI] Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP.[HAMAP-Rule:MF_00072]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 __TOC__
 </SX>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Bouakaz, L]]
+[[Category: Bouakaz L]]
-[[Category: Ehrenberg, M]]
+[[Category: Ehrenberg M]]
-[[Category: Frank, J]]
+[[Category: Frank J]]
-[[Category: Gao, H]]
+[[Category: Gao H]]
-[[Category: Gursky, R]]
+[[Category: Gursky R]]
-[[Category: Huang, C]]
+[[Category: Huang C]]
-[[Category: Liu, Y]]
+[[Category: Liu Y]]
-[[Category: Rawat, U]]
+[[Category: Rawat U]]
-[[Category: Sanyal, S]]
+[[Category: Sanyal S]]
-[[Category: Song, H]]
+[[Category: Song H]]
-[[Category: Wang, C]]
+[[Category: Wang C]]
-[[Category: Zavialov, A]]
+[[Category: Zavialov A]]
-[[Category: Zhou, Z]]
+[[Category: Zhou Z]]
-[[Category: Cryo-em]]
-[[Category: Rf3]]
-[[Category: Ribosome]]
-[[Category: Translation]]

2o0f

From Proteopedia

Current revision

Docking of the modified RF3 X-ray structure into cryo-EM map of E.coli 70S ribosome bound with RF3

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