2q4g

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(New page: 200px<br /> <applet load="2q4g" size="450" color="white" frame="true" align="right" spinBox="true" caption="2q4g, resolution 1.954&Aring;" /> '''Ensemble refinemen...)
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[[Image:2q4g.gif|left|200px]]<br />
 
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<applet load="2q4g" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2q4g, resolution 1.954&Aring;" />
 
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'''Ensemble refinement of the protein crystal structure of human ribonuclease inhibitor complexed with ribonuclease I'''<br />
 
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==Overview==
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==Ensemble refinement of the protein crystal structure of human ribonuclease inhibitor complexed with ribonuclease I==
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X-ray crystallography typically uses a single set of coordinates and B, factors to describe macromolecular conformations. Refinement of multiple, copies of the entire structure has been previously used in specific cases, as an alternative means of representing structural flexibility. Here, we, systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of, the distributions of atomic positions in the simulated structures than, single-conformer refinements. Comparison of principal components, calculated from the refined ensembles and simulations shows that concerted, motions are captured locally, but that correlations dissipate over long, distances. Ensemble refinement is also used on 50 experimental structures, of varying resolution and leads to decreases in R(free) values, implying, that improvements in the representation of flexibility observed for the, simulated structures may apply to real structures. These gains are, essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from, ensemble refinement.
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<StructureSection load='2q4g' size='340' side='right'caption='[[2q4g]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2q4g]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4G 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]] 1.954&#8491;, 8 models</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=CIT:CITRIC+ACID'>CIT</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=2q4g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4g OCA], [https://pdbe.org/2q4g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4g RCSB], [https://www.ebi.ac.uk/pdbsum/2q4g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4g ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNAS1_HUMAN RNAS1_HUMAN] Endonuclease that catalyzes the cleavage of RNA on the 3' side of pyrimidine nucleotides. Acts on single stranded and double stranded RNA.<ref>PMID:17350650</ref>
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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/q4/2q4g_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2q4g 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 ribonuclease inhibitor protein (RI) binds to members of the bovine pancreatic ribonuclease (RNase A) superfamily with an affinity in the femtomolar range. Here, we report on structural and energetic aspects of the interaction between human RI (hRI) and human pancreatic ribonuclease (RNase 1). The structure of the crystalline hRI x RNase 1 complex was determined at a resolution of 1.95 A, revealing the formation of 19 intermolecular hydrogen bonds involving 13 residues of RNase 1. In contrast, only nine such hydrogen bonds are apparent in the structure of the complex between porcine RI and RNase A. hRI, which is anionic, also appears to use its horseshoe-shaped structure to engender long-range Coulombic interactions with RNase 1, which is cationic. In accordance with the structural data, the hRI.RNase 1 complex was found to be extremely stable (t(1/2)=81 days; K(d)=2.9 x 10(-16) M). Site-directed mutagenesis experiments enabled the identification of two cationic residues in RNase 1, Arg39 and Arg91, that are especially important for both the formation and stability of the complex, and are thus termed "electrostatic targeting residues". Disturbing the electrostatic attraction between hRI and RNase 1 yielded a variant of RNase 1 that maintained ribonucleolytic activity and conformational stability but had a 2.8 x 10(3)-fold lower association rate for complex formation and 5.9 x 10(9)-fold lower affinity for hRI. This variant of RNase 1, which exhibits the largest decrease in RI affinity of any engineered ribonuclease, is also toxic to human erythroleukemia cells. Together, these results provide new insight into an unusual and important protein-protein interaction, and could expedite the development of human ribonucleases as chemotherapeutic agents.
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==Disease==
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Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein.,Johnson RJ, McCoy JG, Bingman CA, Phillips GN Jr, Raines RT J Mol Biol. 2007 Apr 27;368(2):434-49. Epub 2007 Feb 9. PMID:17350650<ref>PMID:17350650</ref>
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Known diseases associated with this structure: Creutzfeldt-Jakob disease OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176640 176640]], Gerstmann-Straussler disease OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176640 176640]], Huntington disease-like 1 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176640 176640]], Insomnia, fatal familial OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176640 176640]], Prion disease with protracted course OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=176640 176640]]
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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2Q4G is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with CIT as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Pancreatic_ribonuclease Pancreatic ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.5 3.1.27.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2Q4G OCA].
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</div>
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<div class="pdbe-citations 2q4g" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17850744 17850744]
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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*[[Ribonuclease inhibitor|Ribonuclease inhibitor]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Pancreatic ribonuclease]]
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[[Category: Large Structures]]
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[[Category: Protein complex]]
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[[Category: Kondrashov DA]]
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[[Category: CESG, Center.for.Eukaryotic.Structural.Genomics.]]
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[[Category: Levin EJ]]
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[[Category: Jr., G.N.Phillips.]]
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[[Category: Phillips Jr GN]]
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[[Category: Kondrashov, D.A.]]
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[[Category: Wesenberg GE]]
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[[Category: Levin, E.J.]]
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[[Category: Wesenberg, G.E.]]
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[[Category: CIT]]
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[[Category: center for eukaryotic structural genomics]]
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[[Category: cesg]]
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[[Category: ensemble refinement]]
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[[Category: enzyme-inhibitor complex]]
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[[Category: hydrolase/hydrolase inhibitor complex]]
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[[Category: leucine-rich repeat]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: refinement methodology development]]
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[[Category: ribonuclease-inhibitor complex]]
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[[Category: structural genomics]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:29:26 2007''
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Current revision

Ensemble refinement of the protein crystal structure of human ribonuclease inhibitor complexed with ribonuclease I

PDB ID 2q4g

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