View source for 3eda


==Carbonmonoxy Sperm Whale Myoglobin at 100 K: Laser on [150 min]==
<StructureSection load='3eda' size='340' side='right'caption='[[3eda]], [[Resolution|resolution]] 1.21&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3eda]] 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=3EDA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EDA FirstGlance]. <br>
</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>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3e55|3e55]], [[3ecx|3ecx]]</div></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=3eda FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eda OCA], [https://pdbe.org/3eda PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eda RCSB], [https://www.ebi.ac.uk/pdbsum/3eda PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eda 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/3eda_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=3eda 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.

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 3eda" style="background-color:#fffaf0;"></div>

==See Also==
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Physeter catodon]]
[[Category: Adachi, S]]
[[Category: Chollet, M]]
[[Category: Ichikawa, H]]
[[Category: Ichiyanagi, K]]
[[Category: Kawai, F]]
[[Category: Koshihara, S]]
[[Category: Nozawa, S]]
[[Category: Park, S Y]]
[[Category: Sato, T]]
[[Category: Tomita, A]]
[[Category: Haem protein]]
[[Category: Heme]]
[[Category: Iron]]
[[Category: Ligand migration]]
[[Category: Metal-binding]]
[[Category: Muscle protein]]
[[Category: Myoglobin]]
[[Category: Oxygen transport]]
[[Category: Photodissociation]]
[[Category: Transport]]