5ndc: Difference between revisions
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The | ==Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography== | ||
<StructureSection load='5ndc' size='340' side='right'caption='[[5ndc]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ndc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NDC 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]] 2.3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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=5ndc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ndc OCA], [https://pdbe.org/5ndc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ndc RCSB], [https://www.ebi.ac.uk/pdbsum/5ndc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ndc ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba 3-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 A resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba 3-type and aa 3-type cytochrome c oxidases around the proton-loading site are also described. | |||
Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature.,Andersson R, Safari C, Dods R, Nango E, Tanaka R, Yamashita A, Nakane T, Tono K, Joti Y, Bath P, Dunevall E, Bosman R, Nureki O, Iwata S, Neutze R, Branden G Sci Rep. 2017 Jul 3;7(1):4518. doi: 10.1038/s41598-017-04817-z. PMID:28674417<ref>PMID:28674417</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5ndc" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermus thermophilus]] | |||
[[Category: Andersson R]] | |||
[[Category: Bath P]] | |||
[[Category: Bosman E]] | |||
[[Category: Branden G]] | |||
[[Category: Dods R]] | |||
[[Category: Dunevall E]] | |||
[[Category: Iwata S]] | |||
[[Category: Joti Y]] | |||
[[Category: Nakane T]] | |||
[[Category: Nango E]] | |||
[[Category: Neutze R]] | |||
[[Category: Nureki O]] | |||
[[Category: Safari C]] | |||
[[Category: Tanaka R]] | |||
[[Category: Tono K]] | |||
Latest revision as of 15:48, 15 November 2023
Structure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallographyStructure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography
Structural highlights
FunctionPublication Abstract from PubMedCytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba 3-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 A resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba 3-type and aa 3-type cytochrome c oxidases around the proton-loading site are also described. Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature.,Andersson R, Safari C, Dods R, Nango E, Tanaka R, Yamashita A, Nakane T, Tono K, Joti Y, Bath P, Dunevall E, Bosman R, Nureki O, Iwata S, Neutze R, Branden G Sci Rep. 2017 Jul 3;7(1):4518. doi: 10.1038/s41598-017-04817-z. PMID:28674417[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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