1vy5: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1vy5]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcq 4qcq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcr 4qcr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcs 4qcs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qct 4qct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VY5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[1vy5]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcq 4qcq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcr 4qcr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcs 4qcs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qct 4qct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VY5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VY5 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=31M:3-DEOXY-3-[(L-METHIONYL-L-PHENYLALANYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31M</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 2.55Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=31M:3-DEOXY-3-[(L-METHIONYL-L-PHENYLALANYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31M</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1vy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vy5 OCA], [https://pdbe.org/1vy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vy5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vy5 ProSAT]</span></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=1vy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vy5 OCA], [https://pdbe.org/1vy5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vy5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vy5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vy5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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==See Also== | ==See Also== | ||
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]] | |||
*[[Ribosome 3D structures|Ribosome 3D structures]] | |||
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | ||
== References == | == References == | ||
Latest revision as of 03:06, 28 December 2023
Crystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated tRNA in the P site.Crystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated tRNA in the P site.
Structural highlights
FunctionRS4_THET8 One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] Publication Abstract from PubMedDuring peptide-bond formation on the ribosome, the alpha-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-A resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.,Polikanov YS, Steitz TA, Innis CA Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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