8ud8

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'''Unreleased structure'''
 
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The entry 8ud8 is ON HOLD
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==Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution==
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<StructureSection load='8ud8' size='340' side='right'caption='[[8ud8]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
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Authors: Aleksandrova, E.V., Syroegin, E.A., Wu, K.J.Y., Tresco, B.I.C., Ramkissoon, A., See, D.N.Y., Liow, P., Dittemore, G.A., Yu, M., Testolin, G., Mitcheltree, M.J., Liu, R.Y., Svetlov, M.S., Myers, A.G., Polikanov, Y.S.
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== Structural highlights ==
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<table><tr><td colspan='2'>[[8ud8]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8UD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8UD8 FirstGlance]. <br>
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Description: Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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[[Category: Unreleased Structures]]
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=31H:3-DEOXY-3-[(N-FORMYL-L-METHIONYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31H</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</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=8AH:5-O-(dihydroxyphosphanyl)-2,8-dimethyladenosine'>8AH</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</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=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=WC9:(4S,5aS,8S,8aR)-4-(2-methylpropyl)-N-[(1R,5Z,7R,8R,9R,10R,11S,12R)-10,11,12-trihydroxy-7-methyl-13-oxa-2-thiabicyclo[7.3.1]tridec-5-en-8-yl]octahydro-2H-oxepino[2,3-c]pyrrole-8-carboxamide+(non-preferred+name)'>WC9</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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[[Category: See, D.N.Y]]
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8ud8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ud8 OCA], [https://pdbe.org/8ud8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ud8 RCSB], [https://www.ebi.ac.uk/pdbsum/8ud8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ud8 ProSAT]</span></td></tr>
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[[Category: Liow, P]]
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</table>
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[[Category: Polikanov, Y.S]]
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== Function ==
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[[Category: Mitcheltree, M.J]]
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[https://www.uniprot.org/uniprot/RL5_THET8 RL5_THET8] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (forming bridge B1b) connecting the head of the 30S subunit to the top of the 50S subunit. The bridge itself contacts the P site tRNA and is implicated in movement during ribosome translocation. Also contacts the P site tRNA independently of the intersubunit bridge; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B]
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[[Category: Testolin, G]]
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__TOC__
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[[Category: Yu, M]]
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</StructureSection>
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[[Category: Syroegin, E.A]]
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[[Category: Large Structures]]
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[[Category: Svetlov, M.S]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: Tresco, B.I.C]]
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[[Category: Aleksandrova EV]]
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[[Category: Liu, R.Y]]
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[[Category: Dittemore GA]]
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[[Category: Dittemore, G.A]]
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[[Category: Liow P]]
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[[Category: Ramkissoon, A]]
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[[Category: Liu RY]]
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[[Category: Wu, K.J.Y]]
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[[Category: Mitcheltree MJ]]
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[[Category: Myers, A.G]]
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[[Category: Myers AG]]
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[[Category: Aleksandrova, E.V]]
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[[Category: Polikanov YS]]
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[[Category: Ramkissoon A]]
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[[Category: See DNY]]
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[[Category: Svetlov MS]]
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[[Category: Syroegin EA]]
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[[Category: Testolin G]]
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[[Category: Tresco BIC]]
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[[Category: Wu KJY]]
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[[Category: Yu M]]

Revision as of 08:59, 21 February 2024

Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with cresomycin, mRNA, deacylated A-site tRNAphe, aminoacylated P-site fMet-tRNAmet, and deacylated E-site tRNAphe at 2.70A resolution

PDB ID 8ud8

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