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1q86

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(New page: 200px<br /><applet load="1q86" size="450" color="white" frame="true" align="right" spinBox="true" caption="1q86, resolution 3.00&Aring;" /> '''Crystal structure of...)
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[[Image:1q86.jpg|left|200px]]<br /><applet load="1q86" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1q86, resolution 3.00&Aring;" />
 
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'''Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.'''<br />
 
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==Overview==
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==Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.==
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The large ribosomal subunit catalyzes peptide bond formation and will do, so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have, refined at 3-A resolution the structures of both A and P site substrate, and product analogues, as well as an intermediate analogue, bound to the, Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the, presence of sparsomycin binds only to the P site. The CCA portions of, these analogues are bound identically by either the A or P loop of the 23S, rRNA. Combining the separate P and A site substrate complexes into one, model reveals interactions that may occur when both are present, simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the, A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a, second hydrogen bond either with the 2' OH of the A-76 ribose in the P, site or with the 2' OH of A2486 (2451). These interactions position the, alpha amino group adjacent to the carbonyl carbon of esterified P site, substrate in an orientation suitable for a nucleophilic attack.
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<StructureSection load='1q86' size='340' side='right'caption='[[1q86]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1q86]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q86 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q86 FirstGlance]. <br>
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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]] 3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PHA:PHENYLALANINAL'>PHA</scene></td></tr>
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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=1q86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q86 OCA], [https://pdbe.org/1q86 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q86 RCSB], [https://www.ebi.ac.uk/pdbsum/1q86 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q86 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q8/1q86_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1q86 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.
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==About this Structure==
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Structural insights into peptide bond formation.,Hansen JL, Schmeing TM, Moore PB, Steitz TA Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11670-5. Epub 2002 Aug 16. PMID:12185246<ref>PMID:12185246</ref>
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1Q86 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui] with MG, K, NA, CD, CL and PHA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q86 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural insights into peptide bond formation., Hansen JL, Schmeing TM, Moore PB, Steitz TA, Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11670-5. Epub 2002 Aug 16. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12185246 12185246]
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</div>
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[[Category: Haloarcula marismortui]]
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<div class="pdbe-citations 1q86" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Hansen, J.L.]]
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[[Category: Moore, P.B.]]
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[[Category: Schmeing, M.T.]]
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[[Category: Steitz, T.A.]]
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[[Category: CD]]
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[[Category: CL]]
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[[Category: K]]
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[[Category: MG]]
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[[Category: NA]]
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[[Category: PHA]]
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[[Category: a-site]]
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[[Category: p-site]]
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[[Category: protein-protein complex]]
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[[Category: protein-rna complex]]
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[[Category: ribosome 50s]]
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[[Category: rna-rna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:28:36 2007''
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==See Also==
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Haloarcula marismortui]]
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[[Category: Large Structures]]
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[[Category: Hansen JL]]
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[[Category: Moore PB]]
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[[Category: Schmeing TM]]
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[[Category: Steitz TA]]

Current revision

Crystal structure of CCA-Phe-cap-biotin bound simultaneously at half occupancy to both the A-site and P-site of the the 50S ribosomal Subunit.

PDB ID 1q86

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