1x8o: Difference between revisions

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-[[Image:1x8o.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1x8o", creates the "Structure Box" on the page.
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-{{STRUCTURE_1x8o|  PDB=1x8o  |  SCENE=  }}
-'''1.01 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6'''
+==1.01 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 5.6==
+<StructureSection load='1x8o' size='340' side='right'caption='[[1x8o]], [[Resolution|resolution]] 1.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1x8o]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X8O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X8O FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.01&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1x8o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x8o OCA], [https://pdbe.org/1x8o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x8o RCSB], [https://www.ebi.ac.uk/pdbsum/1x8o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x8o ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NP4_RHOPR NP4_RHOPR] Heme-based protein that deliver nitric oxide gas (NO) to the victim while feeding, resulting in vasodilation and inhibition of platelet aggregation. Also bind tightly to histamine, which is released by the host to induce wound healing (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x8/1x8o_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1x8o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The blood-sucking insect Rhodnius prolixus uses nitrophorin 4, a heme protein, to deliver nitric oxide (NO) to a victim, causing vasodilation and improved feeding. Binding of NO occurs at a ferric heme and is modulated by pH. NO binding at lower pH induces a large conformational change involving loops A-B and G-H that leads to distal pocket desolvation and protection of the nitrosyl heme complex. We have determined the crystal structures of Rhodnius nitrophorin 4 to ultrahigh resolution in four functional states: +/-NO at pH = 7.4 and +/-NO at pH = 5.6. The structure with NO at pH 7.4 (1.08 A) is newly determined while the other complexes have been modeled to resolutions much greater than previously reported (1.0-0.85 A). The ultrahigh resolution allowed us to resolve multiple conformers in binding-site loops, leading to a detailed description of the dynamics involved with storing NO in the insect salivary gland at low pH, and releasing NO in response to the increased pH of a victim's tissue. Strikingly, features for both the "open" and "closed" conformers exist under all conditions, suggesting that the flexible loops can transition with relative ease between conformational states. Yet, release of NO from rNP4 is much slower than found for other ferric heme proteins. The structures suggest that highly mobile loops can limit diffusion of diatomic molecules into and out of a protein cavity, a result with implications for the role of protein dynamics in function.
-==Overview==
+Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding.,Kondrashov DA, Roberts SA, Weichsel A, Montfort WR Biochemistry. 2004 Nov 2;43(43):13637-47. PMID:15504026<ref>PMID:15504026</ref>
-The blood-sucking insect Rhodnius prolixus uses nitrophorin 4, a heme protein, to deliver nitric oxide (NO) to a victim, causing vasodilation and improved feeding. Binding of NO occurs at a ferric heme and is modulated by pH. NO binding at lower pH induces a large conformational change involving loops A-B and G-H that leads to distal pocket desolvation and protection of the nitrosyl heme complex. We have determined the crystal structures of Rhodnius nitrophorin 4 to ultrahigh resolution in four functional states: +/-NO at pH = 7.4 and +/-NO at pH = 5.6. The structure with NO at pH 7.4 (1.08 A) is newly determined while the other complexes have been modeled to resolutions much greater than previously reported (1.0-0.85 A). The ultrahigh resolution allowed us to resolve multiple conformers in binding-site loops, leading to a detailed description of the dynamics involved with storing NO in the insect salivary gland at low pH, and releasing NO in response to the increased pH of a victim's tissue. Strikingly, features for both the "open" and "closed" conformers exist under all conditions, suggesting that the flexible loops can transition with relative ease between conformational states. Yet, release of NO from rNP4 is much slower than found for other ferric heme proteins. The structures suggest that highly mobile loops can limit diffusion of diatomic molecules into and out of a protein cavity, a result with implications for the role of protein dynamics in function.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-X8O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodnius_prolixus Rhodnius prolixus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X8O OCA].
+</div>
+<div class="pdbe-citations 1x8o" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding., Kondrashov DA, Roberts SA, Weichsel A, Montfort WR, Biochemistry. 2004 Nov 2;43(43):13637-47. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15504026 15504026]
+*[[Nitrophorin|Nitrophorin]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Rhodnius prolixus]]
-[[Category: Single protein]]
+[[Category: Kondrashov DA]]
-[[Category: Kondrashov, D A.]]
+[[Category: Montfort WR]]
-[[Category: Montfort, W R.]]
+[[Category: Roberts SA]]
-[[Category: Roberts, S A.]]
+[[Category: Weichsel A]]
-[[Category: Weichsel, A.]]
-[[Category: Beta barrel]]
-[[Category: Heme]]
-[[Category: Lipocalin]]
-[[Category: Nitric oxide]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 14:42:31 2008''