6j8m
From Proteopedia
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- | '''Unreleased structure''' | ||
- | + | ==Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray== | |
+ | <StructureSection load='6j8m' size='340' side='right'caption='[[6j8m]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
+ | == Structural highlights == | ||
+ | <table><tr><td colspan='2'>[[6j8m]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J8M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J8M 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]] 1.9Å</td></tr> | ||
+ | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CHD:CHOLIC+ACID'>CHD</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEK:(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL+(5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE'>PEK</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene>, <scene name='pdbligand=PGV:(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+(11E)-OCTADEC-11-ENOATE'>PGV</scene>, <scene name='pdbligand=PSC:(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM+4-OXIDE'>PSC</scene>, <scene name='pdbligand=SAC:N-ACETYL-SERINE'>SAC</scene>, <scene name='pdbligand=TGL:TRISTEAROYLGLYCEROL'>TGL</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6j8m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j8m OCA], [https://pdbe.org/6j8m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j8m RCSB], [https://www.ebi.ac.uk/pdbsum/6j8m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j8m ProSAT]</span></td></tr> | ||
+ | </table> | ||
+ | == Function == | ||
+ | [https://www.uniprot.org/uniprot/COX3_BOVIN COX3_BOVIN] Subunits I, II and III form the functional core of the enzyme complex. | ||
+ | <div style="background-color:#fffaf0;"> | ||
+ | == Publication Abstract from PubMed == | ||
+ | To investigate the effect of high-energy X-rays on site-specific radiation-damage, low-dose diffraction data were collected from radiation-sensitive crystals of the metal enzyme cytochrome c oxidase. Data were collected at the Structural Biology I beamline (BL41XU) at SPring-8, using 30 keV X-rays and a highly sensitive pixel array detector equipped with a cadmium telluride sensor. The experimental setup of continuous sample translation using multiple crystals allowed the average diffraction weighted dose per data set to be reduced to 58 kGy, and the resulting data revealed a ligand structure featuring an identical bond length to that in the damage-free structure determined using an X-ray free-electron laser. However, precise analysis of the residual density around the ligand structure refined with the synchrotron data showed the possibility of a small level of specific damage, which might have resulted from the accumulated dose of 58 kGy per data set. Further investigation of the photon-energy dependence of specific damage, as assessed by variations in UV-vis absorption spectra, was conducted using an on-line spectrometer at various energies ranging from 10 to 30 keV. No evidence was found for specific radiation damage being energy dependent. | ||
- | + | Low-dose X-ray structure analysis of cytochrome c oxidase utilizing high-energy X-rays.,Ueno G, Shimada A, Yamashita E, Hasegawa K, Kumasaka T, Shinzawa-Itoh K, Yoshikawa S, Tsukihara T, Yamamoto M J Synchrotron Radiat. 2019 Jul 1;26(Pt 4):912-921. doi:, 10.1107/S1600577519006805. Epub 2019 Jun 14. PMID:31274413<ref>PMID:31274413</ref> | |
- | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
- | [[ | + | </div> |
- | [[Category: | + | <div class="pdbe-citations 6j8m" style="background-color:#fffaf0;"></div> |
- | [[Category: | + | |
- | [[Category: Hasegawa | + | ==See Also== |
- | [[Category: Kumasaka | + | *[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]] |
- | [[Category: | + | == References == |
- | [[Category: Shinzawa-Itoh | + | <references/> |
- | [[Category: | + | __TOC__ |
- | [[Category: | + | </StructureSection> |
- | [[Category: | + | [[Category: Bos taurus]] |
+ | [[Category: Large Structures]] | ||
+ | [[Category: Hasegawa K]] | ||
+ | [[Category: Kumasaka T]] | ||
+ | [[Category: Shimada A]] | ||
+ | [[Category: Shinzawa-Itoh K]] | ||
+ | [[Category: Tsukihara T]] | ||
+ | [[Category: Ueno G]] | ||
+ | [[Category: Yamamoto M]] | ||
+ | [[Category: Yamashita E]] | ||
+ | [[Category: Yoshikawa S]] |
Current revision
Low-dose structure of bovine heart cytochrome c oxidase in the fully oxidized state determined using 30 keV X-ray
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