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1y69

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RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans

Structural highlights

1y69 is a 5 chain structure with sequence from Deinococcus radiodurans R1 and Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.33Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL16_DEIRA Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center.[HAMAP-Rule:MF_01342]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

This study presents the crystal structure of domain I of the Escherichia coli ribosome recycling factor (RRF) bound to the Deinococcus radiodurans 50S subunit. The orientation of RRF is consistent with the position determined on a 70S-RRF complex by cryoelectron microscopy (cryo-EM). Alignment, however, requires a rotation of 7 degrees and a shift of the cryo-EM RRF by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. At 3.3 A resolution, RRF is seen to interact exclusively with ribosomal elements associated with tRNA binding and/or translocation. Furthermore, these results now provide a high-resolution structural description of the conformational changes that were suspected to occur on the 70S-RRF complex, which has implications for the synergistic action of RRF with elongation factor G (EF-G). Specifically, the tip of the universal bridge element H69 is shifted by 20 A toward h44 of the 30S subunit, suggesting that RRF primes the intersubunit bridge B2a for the action of EF-G. Collectively, our data enable a model to be proposed for the dual action of EF-G and RRF during ribosome recycling.

X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.,Wilson DN, Schluenzen F, Harms JM, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y, Fucini P EMBO J. 2005 Jan 26;24(2):251-60. Epub 2004 Dec 23. PMID:15616575^[1]

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

References

↑ Wilson DN, Schluenzen F, Harms JM, Yoshida T, Ohkubo T, Albrecht R, Buerger J, Kobayashi Y, Fucini P. X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit. EMBO J. 2005 Jan 26;24(2):251-60. Epub 2004 Dec 23. PMID:15616575

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/1y69"

@@ Line 3: / Line 3: @@
 <StructureSection load='1y69' size='340' side='right'caption='[[1y69]], [[Resolution|resolution]] 3.33&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1y69]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/ ], [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_(strain_atcc_13939_/_dsm_20539_/_jcm_16871_/_lmg_4051_/_nbrc_15346_/_ncimb_9279_/_r1_/_vkm_b-1422) Deinococcus radiodurans (strain atcc 13939 / dsm 20539 / jcm 16871 / lmg 4051 / nbrc 15346 / ncimb 9279 / r1 / vkm b-1422)] and [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_r1 Deinococcus radiodurans r1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y69 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1y69]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1] and [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y69 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y69 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;'>[[1nkw|1nkw]], [[1ek8|1ek8]]</div></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]] 3.33&#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=1y69 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y69 OCA], [https://pdbe.org/1y69 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y69 RCSB], [https://www.ebi.ac.uk/pdbsum/1y69 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y69 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RL27_DEIRA RL27_DEIRA]] Binds the 5S and 23S rRNAs and also the tRNA in the P site.[HAMAP-Rule:MF_00539] [[https://www.uniprot.org/uniprot/RL16_DEIRA RL16_DEIRA]] Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center.[HAMAP-Rule:MF_01342] [[https://www.uniprot.org/uniprot/RRF_ECOLI RRF_ECOLI]] Responsible for the release of ribosomes from messenger RNA at the termination of protein biosynthesis. May increase the efficiency of translation by recycling ribosomes from one round of translation to another.[HAMAP-Rule:MF_00040]
+[https://www.uniprot.org/uniprot/RL16_DEIRA RL16_DEIRA] Binds the 5S and 23S rRNAs and is also seen to make contacts with the A and P site tRNAs. Interacts with A site tRNA mimics, and is probably one of the key factors, along with a helix of the 23S rRNA, in positioning tRNA stems in the peptidyl-transferase center.[HAMAP-Rule:MF_01342]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Deinococcus radiodurans r1]]
+[[Category: Deinococcus radiodurans R1]]
+[[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
-[[Category: Albrecht, R]]
+[[Category: Albrecht R]]
-[[Category: Buerger, J]]
+[[Category: Buerger J]]
-[[Category: Fucini, P]]
+[[Category: Fucini P]]
-[[Category: Harms, J M]]
+[[Category: Harms JM]]
-[[Category: Kobayashi, Y]]
+[[Category: Kobayashi Y]]
-[[Category: Ohkubo, T]]
+[[Category: Ohkubo T]]
-[[Category: Schluenzen, F]]
+[[Category: Schluenzen F]]
-[[Category: Wilson, D N]]
+[[Category: Wilson DN]]
-[[Category: Yoshida, T]]
+[[Category: Yoshida T]]
-[[Category: Recycling factor]]
-[[Category: Ribosome]]
-[[Category: Rrf]]

1y69

From Proteopedia

Current revision

RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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