1bc4: Difference between revisions

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 ==THE SOLUTION STRUCTURE OF A CYTOTOXIC RIBONUCLEASE FROM THE OOCYTES OF RANA CATESBEIANA (BULLFROG), NMR, 15 STRUCTURES==
-<StructureSection load='1bc4' size='340' side='right'caption='[[1bc4]], [[NMR_Ensembles_of_Models | 15 NMR models]]' scene=''>
+<StructureSection load='1bc4' size='340' side='right'caption='[[1bc4]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1bc4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rana_catesbeiana Rana catesbeiana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BC4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1bc4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lithobates_catesbeianus Lithobates catesbeianus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BC4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BC4 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</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=1bc4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bc4 OCA], [https://pdbe.org/1bc4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bc4 RCSB], [https://www.ebi.ac.uk/pdbsum/1bc4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bc4 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RNASO_LITCT RNASO_LITCT]] Preferentially cleaves single-stranded RNA at pyrimidine residues with a 3'flanking guanine. Hydrolyzes poly(U) and poly(C) as substrates, and prefers the former. The S-lectins in frog eggs may be involved in the fertilization and development of the frog embryo. This lectin agglutinates various animal cells, including normal lymphocytes, erythrocytes, and fibroblasts of animal and human origin. It is cytotoxic against several tumor cells.
+[https://www.uniprot.org/uniprot/RNASO_LITCT RNASO_LITCT] Preferentially cleaves single-stranded RNA at pyrimidine residues with a 3'flanking guanine. Hydrolyzes poly(U) and poly(C) as substrates, and prefers the former. The S-lectins in frog eggs may be involved in the fertilization and development of the frog embryo. This lectin agglutinates various animal cells, including normal lymphocytes, erythrocytes, and fibroblasts of animal and human origin. It is cytotoxic against several tumor cells.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=1bc4 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a lectin possessing potent cell cytotoxicity. It was isolated from the oocytes of Rana catesbeiana (bull frog). From analysis of an extensive set of 1H homonuclear 2D NMR spectra we have completed the resonance assignments. Determination of the three-dimensional structure was carried out with the program X-PLOR using a total of 951 restraints including 814 NMR-derived distances, 61 torsion angles, and 76 hydrogen bond restraints. In the resultant family of 15 best structures, selected from a total of 150 calculated structures, the root-mean-square deviation from the average structure for the backbone heavy-atoms involved in well-defined secondary structure is 0.48 A, while that for all backbone heavy-atoms is 0.91 A. The structure of RC-RNase consists of three alpha-helices and two triple-stranded anti-parallel beta-sheets and folds in a kidney-shape, very similar to the X-ray crystal structure of a homolo gous protein, onconase isolated from Rana pipiens. We have also investigated the interaction between RC-RNase and two inhibitors, cytidylyl(2'--&gt;5')guanosine (2',5'-CpG) and 2'-deoxycytidylyl(3'--&gt;5')-2'-deoxyguanosine (3',5'-dCpdG). Based on the ligand-induced chemical shift changes in RC-RNase and the NOE cross-peaks between RC-RNase and the inhibitors, the key residues involved in protein-inhibitor interaction have been identified. The inhibitors were found to bind in a "retro-binding" mode, with the guanine base bonded to the B1 subsite. The His103 residue was found to occupy the B state with the imidazole ring pointing away from the active site. The structure coordinates and the NMR restraints have been deposited in the Brookhaven Protein Data Bank (1bc4 and 1bc4mr, respectively).
-The solution structure of a cytotoxic ribonuclease from the oocytes of Rana catesbeiana (bullfrog).,Chang CF, Chen C, Chen YC, Hom K, Huang RF, Huang TH J Mol Biol. 1998;283(1):231-44. PMID:9761686<ref>PMID:9761686</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1bc4" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Pancreatic ribonuclease]]
+[[Category: Lithobates catesbeianus]]
-[[Category: Rana catesbeiana]]
+[[Category: Chang C-F]]
-[[Category: Chang, C F]]
+[[Category: Chen C]]
-[[Category: Chen, C]]
+[[Category: Chen Y-C]]
-[[Category: Chen, Y C]]
+[[Category: Hom K]]
-[[Category: Hom, K]]
+[[Category: Huang R-F]]
-[[Category: Huang, R F]]
+[[Category: Huang T]]
-[[Category: Huang, T]]
-[[Category: Cytotoxic protein]]
-[[Category: Hydrolase]]
-[[Category: Phosphoric diester]]
-[[Category: Rc-rnase]]
-[[Category: Sialic acid binding lectin]]