4v79: Difference between revisions

Latest revision as of 13:27, 1 July 2026

E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b)

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Structural highlights

4v79 is a 10 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 15Å
Ligands:	4SU, 5MU, 6MZ, 7MG, ACE, CM0, FME, H2U, NH2, OMC, PSU, VAL
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS2_ECOLI

Publication Abstract from PubMed

During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.

Energy barriers and driving forces in tRNA translocation through the ribosome.,Bock LV, Blau C, Schroder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmuller H Nat Struct Mol Biol. 2013 Nov 3. doi: 10.1038/nsmb.2690. PMID:24186064^[1]

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

References

↑ Bock LV, Blau C, Schroder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmuller H. Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol. 2013 Nov 3. doi: 10.1038/nsmb.2690. PMID:24186064 doi:https://dx.doi.org/10.1038/nsmb.2690

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OCA

[1] Bock LV, Blau C, Schroder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmuller H. Energy barriers and driving forces in tRNA translocation through the ribosome. Nat Struct Mol Biol. 2013 Nov 3. doi: 10.1038/nsmb.2690. PMID:24186064 doi:https://dx.doi.org/10.1038/nsmb.2690

[1]

@@ Line 3: / Line 3: @@
 <SX load='4v79' size='340' side='right' viewer='molstar' caption='[[4v79]], [[Resolution|resolution]] 15.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4v79]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j5h 3j5h] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3j5i 3j5i]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V79 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4v79]] is a 10 chain structure with sequence from [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=4V79 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V79 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene></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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</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=4v79 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v79 OCA], [https://pdbe.org/4v79 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v79 RCSB], [https://www.ebi.ac.uk/pdbsum/4v79 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v79 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/RL29_ECOLI RL29_ECOLI] Binds 23S rRNA. It is not essential for growth.[HAMAP-Rule:MF_00374]  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (PubMed:12226666).[HAMAP-Rule:MF_00374]
+[https://www.uniprot.org/uniprot/RS2_ECOLI RS2_ECOLI]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

4v79: Difference between revisions

Latest revision as of 13:27, 1 July 2026

E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b)

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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