3edb: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3edb.png|left|200px]]
-<!--
+==Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [150 min]==
-The line below this paragraph, containing "STRUCTURE_3edb", creates the "Structure Box" on the page.
+<StructureSection load='3edb' size='340' side='right'caption='[[3edb]], [[Resolution|resolution]] 1.21&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'>[[3edb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EDB 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]] 1.21&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3edb|  PDB=3edb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3edb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3edb OCA], [https://pdbe.org/3edb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3edb RCSB], [https://www.ebi.ac.uk/pdbsum/3edb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3edb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYG_PHYMC MYG_PHYMC] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
+== 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/ed/3edb_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3edb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.
-===Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [150 min]===
+Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin.,Tomita A, Sato T, Ichiyanagi K, Nozawa S, Ichikawa H, Chollet M, Kawai F, Park SY, Tsuduki T, Yamato T, Koshihara SY, Adachi SI Proc Natl Acad Sci U S A. 2009 Feb 9. PMID:19204297<ref>PMID:19204297</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3edb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19204297}}, adds the Publication Abstract to the page
+*[[Myoglobin 3D structures|Myoglobin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19204297 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19204297}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-EDB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Physeter_catodon Physeter catodon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EDB OCA].
-==Reference==
-Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin., Tomita A, Sato T, Ichiyanagi K, Nozawa S, Ichikawa H, Chollet M, Kawai F, Park SY, Tsuduki T, Yamato T, Koshihara SY, Adachi SI, Proc Natl Acad Sci U S A. 2009 Feb 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19204297 19204297]
 [[Category: Physeter catodon]]
-[[Category: Single protein]]
+[[Category: Adachi S]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Chollet M]]
-[[Category: Haem protein]]
+[[Category: Ichikawa H]]
-[[Category: Heme]]
+[[Category: Ichiyanagi K]]
-[[Category: Iron]]
+[[Category: Kawai F]]
-[[Category: Ligand migration]]
+[[Category: Koshihara S]]
-[[Category: Metal-binding]]
+[[Category: Nozawa S]]
-[[Category: Muscle protein]]
+[[Category: Park S-Y]]
-[[Category: Myoglobin]]
+[[Category: Sato T]]
-[[Category: Oxygen transport]]
+[[Category: Tomita A]]
-[[Category: Photodissociation]]
-[[Category: Transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 11 20:12:52 2009''