4emf: Difference between revisions

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-[[Image:4emf.jpg|left|200px]]
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+==Crystal structure of the complex of type I Ribosome inactivating protein in complex with 7n-methyl-8-hydroguanosine-5-p-diphosphate at 1.77 A==
-The line below this paragraph, containing "STRUCTURE_4emf", creates the "Structure Box" on the page.
+<StructureSection load='4emf' size='340' side='right'caption='[[4emf]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[4emf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Momordica_balsamina Momordica balsamina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EMF FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=M7G:7N-METHYL-8-HYDROGUANOSINE-5-DIPHOSPHATE'>M7G</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_4emf|  PDB=4emf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4emf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4emf OCA], [https://pdbe.org/4emf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4emf RCSB], [https://www.ebi.ac.uk/pdbsum/4emf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4emf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/D9J2T9_MOMBA D9J2T9_MOMBA]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+This is the first structural evidence of recognition of mRNA cap structures by a ribosome inactivating protein. It is well known that a unique cap structure is formed at the 5' end of mRNA for carrying out various processes including mRNA maturation, translation initiation, and RNA turnover. The binding studies and crystal structure determinations of type 1 ribosome inactivating protein (RIP-1) from Momordica balsamina (MbRIP-1) were carried out with mRNA cap structures including (i) N7-methyl guanine (m7G), (ii) N7-methyl guanosine diphosphate (m7GDP), and (iii) N7-methyl guanosine triphosphate (m7GTP). These compounds showed affinities to MbRIP-1 at nanomolar concentrations. The structure determinations of the complexes of MbRIP-1 with m7G, m7GDP, and m7GTP at 2.65, 1.77, and 1.75 A resolutions revealed that all the three compounds bound to MbRIP-1 in the substrate binding site at the positions which are slightly shifted towards Glu85 as compared to those of rRNA substrates. In this position, Glu85 forms several hydrogen bonds with guanine moiety while N-7 methyl group forms van der Waals contacts. However, the guanine rings are poorly stacked in these complexes. Thus, the mode of binding by MbRIP-1 to mRNA cap structures is different which results in the inhibition of depurination. Since some viruses are known to exploit the capping property of the host, this action of MbRIP-1 may have implications for the antiviral activity of this protein in vivo. The understanding of the mode of binding of MbRIP-1 to cap structures may also assist in the design of anti-viral agents.
-===Crystal structure of the complex of type I Ribosome inactivating protein in complex with 7n-methyl-8-hydroguanosine-5-p-diphosphate at 1.77 A===
+First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina.,Kushwaha GS, Yamini S, Kumar M, Sinha M, Kaur P, Sharma S, Singh TP Proteins. 2013 May;81(5):896-905. doi: 10.1002/prot.24248. Epub 2013 Feb 25. PMID:23280611<ref>PMID:23280611</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4emf" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[4emf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Momordica_balsamina Momordica balsamina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4EMF OCA].
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Momordica balsamina]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Kaur P]]
-[[Category: Kaur, P.]]
+[[Category: Kushwaha GS]]
-[[Category: Kushwaha, G S.]]
+[[Category: Sharma S]]
-[[Category: Sharma, S.]]
+[[Category: Singh TP]]
-[[Category: Singh, T P.]]
+[[Category: Sinha M]]
-[[Category: Sinha, M.]]
+[[Category: Yamini S]]
-[[Category: Yamini, S.]]
-[[Category: Complex hydrolase]]
-[[Category: Hydrolase]]
-[[Category: Ligand binding]]
-[[Category: Ribosome inactivating protein]]