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5jte

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Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA

5jte, resolution 3.60Å

Structural highlights

5jte is a 10 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 3.6Å
Ligands:
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS5_ECOLI With S4 and S12 plays an important role in translational accuracy. Many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).^[1] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.^[2] The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.^[3]

Publication Abstract from PubMed

Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-A-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.

A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.,Arenz S, Bock LV, Graf M, Innis CA, Beckmann R, Grubmuller H, Vaiana AC, Wilson DN Nat Commun. 2016 Jul 6;7:12026. doi: 10.1038/ncomms12026. PMID:27380950^[4]

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

References

↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Takyar S, Hickerson RP, Noller HF. mRNA helicase activity of the ribosome. Cell. 2005 Jan 14;120(1):49-58. PMID:15652481 doi:10.1016/j.cell.2004.11.042
↑ Arenz S, Bock LV, Graf M, Innis CA, Beckmann R, Grubmuller H, Vaiana AC, Wilson DN. A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest. Nat Commun. 2016 Jul 6;7:12026. doi: 10.1038/ncomms12026. PMID:27380950 doi:http://dx.doi.org/10.1038/ncomms12026

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5jte is ON HOLD
+==Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA==
+<SX load='5jte' size='340' side='right' viewer='molstar' caption='[[5jte]], [[Resolution|resolution]] 3.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5jte]] is a 10 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=5JTE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JTE FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=3AU:3-[(3S)-3-AMINO-3-CARBOXYPROPYL]URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>3AU</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene>, <scene name='pdbligand=ERY:ERYTHROMYCIN+A'>ERY</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=QUO:2-AMINO-7-DEAZA-(2,3-DIHYDROXY-CYCLOPENTYLAMINO)-GUANOSINE-5-MONOPHOSPHATE'>QUO</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</scene>, <scene name='pdbligand=U8U:5-METHYLAMINOMETHYL-2-THIOURIDINE-5-MONOPHOSPHATE'>U8U</scene></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=5jte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jte OCA], [https://pdbe.org/5jte PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jte RCSB], [https://www.ebi.ac.uk/pdbsum/5jte PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jte ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS5_ECOLI RS5_ECOLI] With S4 and S12 plays an important role in translational accuracy. Many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).<ref>PMID:15652481</ref>   Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.<ref>PMID:15652481</ref>   The physical location of this protein suggests it may also play a role in mRNA unwinding by the ribosome, possibly by forming part of a processivity clamp.<ref>PMID:15652481</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nascent polypeptides can induce ribosome stalling, regulating downstream genes. Stalling of ErmBL peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in Streptococcus sanguis. To reveal this stalling mechanism we obtained 3.6-A-resolution cryo-EM structures of ErmBL-stalled ribosomes with erythromycin. The nascent peptide adopts an unusual conformation with the C-terminal Asp10 side chain in a previously unseen rotated position. Together with molecular dynamics simulations, the structures indicate that peptide-bond formation is inhibited by displacement of the peptidyl-tRNA A76 ribose from its canonical position, and by non-productive interactions of the A-tRNA Lys11 side chain with the A-site crevice. These two effects combine to perturb peptide-bond formation by increasing the distance between the attacking Lys11 amine and the Asp10 carbonyl carbon. The interplay between drug, peptide and ribosome uncovered here also provides insight into the fundamental mechanism of peptide-bond formation.
-Authors: Arenz, S., Bock, L.V., Graf, M., Innis, C.A., Beckmann, R., Grubmueller, H., Vaiana, A.C., Wilson, D.N.
+A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.,Arenz S, Bock LV, Graf M, Innis CA, Beckmann R, Grubmuller H, Vaiana AC, Wilson DN Nat Commun. 2016 Jul 6;7:12026. doi: 10.1038/ncomms12026. PMID:27380950<ref>PMID:27380950</ref>
-Description: Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Arenz, S]]
+<div class="pdbe-citations 5jte" style="background-color:#fffaf0;"></div>
-[[Category: Beckmann, R]]
+== References ==
-[[Category: Innis, C.A]]
+<references/>
-[[Category: Graf, M]]
+__TOC__
-[[Category: Bock, L.V]]
+</SX>
-[[Category: Grubmueller, H]]
+[[Category: Escherichia coli]]
-[[Category: Wilson, D.N]]
+[[Category: Large Structures]]
-[[Category: Vaiana, A.C]]
+[[Category: Arenz S]]
+[[Category: Beckmann R]]
+[[Category: Bock LV]]
+[[Category: Graf M]]
+[[Category: Grubmueller H]]
+[[Category: Innis CA]]
+[[Category: Vaiana AC]]
+[[Category: Wilson DN]]

5jte

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Current revision

Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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