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Open data
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Basic information
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Title | E. coli cytochrome bo3 ubiquinol oxidase dimer | |||||||||
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![]() | heme-copper oxidase / proton translocation / E. coli aerobic respiratory chain / membrane protein / PROTON TRANSPORT | |||||||||
Function / homology | ![]() cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / ubiquinone binding / electron transport coupled proton transport ...cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / ubiquinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
![]() | Guo Y / Karimullina E / Borek D / Savchenko A | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Monomer and dimer structures of cytochrome bo ubiquinol oxidase from Escherichia coli. Authors: Yirui Guo / Elina Karimullina / Tabitha Emde / Zbyszek Otwinowski / Dominika Borek / Alexei Savchenko / ![]() ![]() Abstract: The Escherichia coli cytochrome bo ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it ...The Escherichia coli cytochrome bo ubiquinol oxidase is a four-subunit heme-copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts-the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo-EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67-74). | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 121.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19 KB 19 KB | Display Display | ![]() |
Images | ![]() | 82.5 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 226.6 MB 226.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f6cMC ![]() 8f68C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_28879_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28879_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : E. coli Cytochrome bo3 ubiquinol oxidase dimer
Entire | Name: E. coli Cytochrome bo3 ubiquinol oxidase dimer |
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Components |
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-Supramolecule #1: E. coli Cytochrome bo3 ubiquinol oxidase dimer
Supramolecule | Name: E. coli Cytochrome bo3 ubiquinol oxidase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Cytochrome bo(3) ubiquinol oxidase subunit 1
Macromolecule | Name: Cytochrome bo(3) ubiquinol oxidase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ubiquinol oxidase (H+-transporting) |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 73.896875 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVMLL RGFADAIMMR SQQALASAG EAGFLPPHHY DQIFTAHGVI MIFFVAMPFV IGLMNLVVPL QIGARDVAFP FLNNLSFWFT VVGVILVNVS L GVGEFAQT ...String: MFGKLSLDAV PFHEPIVMVT IAGIILGGLA LVGLITYFGK WTYLWKEWLT SVDHKRLGIM YIIVAIVMLL RGFADAIMMR SQQALASAG EAGFLPPHHY DQIFTAHGVI MIFFVAMPFV IGLMNLVVPL QIGARDVAFP FLNNLSFWFT VVGVILVNVS L GVGEFAQT GWLAYPPLSG IEYSPGVGVD YWIWSLQLSG IGTTLTGINF FVTILKMRAP GMTMFKMPVF TWASLCANVL II ASFPILT VTVALLTLDR YLGTHFFTND MGGNMMMYIN LIWAWGHPEV YILILPVFGV FSEIAATFSR KRLFGYTSLV WAT VCITVL SFIVWLHHFF TMGAGANVNA FFGITTMIIA IPTGVKIFNW LFTMYQGRIV FHSAMLWTIG FIVTFSVGGM TGVL LAVPG ADFVLHNSLF LIAHFHNVII GGVVFGCFAG MTYWWPKAFG FKLNETWGKR AFWFWIIGFF VAFMPLYALG FMGMT RRLS QQIDPQFHTM LMIAASGAVL IALGILCLVI QMYVSIRDRD QNRDLTGDPW GGRTLEWATS SPPPFYNFAV VPHVHE RDA FWEMKEKGEA YKKPDHYEEI HMPKNSGAGI VIAAFSTIFG FAMIWHIWWL AIVGFAGMII TWIVKSFDED VDYYVPV AE IEKLENQHFD EITKAG UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 1 |
-Macromolecule #2: Cytochrome bo(3) ubiquinol oxidase subunit 2
Macromolecule | Name: Cytochrome bo(3) ubiquinol oxidase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 28.839297 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GCNSALLDPK GQIGLEQRSL ILTAFGLMLI VVIPAILMAV GFAWKYRASN KDAKYSPNWS HSNKVEAVVW TVPILIIIFL AVLTWKTTH ALEPSKPLAH DEKPITIEVV SMDWKWFFIY PEQGIATVNE IAFPANTPVY FKVTSNSVMN SFFIPRLGSQ I YAMAGMQT ...String: GCNSALLDPK GQIGLEQRSL ILTAFGLMLI VVIPAILMAV GFAWKYRASN KDAKYSPNWS HSNKVEAVVW TVPILIIIFL AVLTWKTTH ALEPSKPLAH DEKPITIEVV SMDWKWFFIY PEQGIATVNE IAFPANTPVY FKVTSNSVMN SFFIPRLGSQ I YAMAGMQT RLHLIANEPG TYDGISASYS GPGFSGMKFK AIATPDRAAF DQWVAKAKQS PNTMSDMAAF EKLAAPSEYN QV EYFSNVK PDLFADVINK FMA UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 2 |
-Macromolecule #3: Cytochrome bo(3) ubiquinol oxidase subunit 3
Macromolecule | Name: Cytochrome bo(3) ubiquinol oxidase subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.464258 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: AGGTKIFGFW IYLMSDCILF SILFATYAVL VNGTAGGPTG KDIFELPFVL VETFLLLFSS ITYGMAAIAM YKNNKSQVIS WLALTWLFG AGFIGMEIYE FHHLIVNGMG PDRSGFLSAF FALVGTHGLH VTSGLIWMAV LMVQIARRGL TSTNRTRIMC L SLFWHFLD VVWICVFTVV YLMGAM UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 3 |
-Macromolecule #4: Cytochrome bo(3) ubiquinol oxidase subunit 4
Macromolecule | Name: Cytochrome bo(3) ubiquinol oxidase subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 10.742083 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SVKTYMTGFI LSIILTVIPF WMVMTGAASP AVILGTILAM AVVQVLVHLV CFLHMNTKSD EGWNMTAFVF TVLIIAILVV GSIWIMWNL NYNMMMH UniProtKB: Cytochrome bo(3) ubiquinol oxidase subunit 4 |
-Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 5 / Number of copies: 2 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ![]() ChemComp-HEM: |
-Macromolecule #6: HEME O
Macromolecule | Name: HEME O / type: ligand / ID: 6 / Number of copies: 2 / Formula: HEO |
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Molecular weight | Theoretical: 838.854 Da |
Chemical component information | ![]() ChemComp-HEO: |
-Macromolecule #7: COPPER (II) ION
Macromolecule | Name: COPPER (II) ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: CU |
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Molecular weight | Theoretical: 63.546 Da |
Chemical component information | ![]() ChemComp-CU: |
-Macromolecule #8: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Macromolecule | Name: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 8 / Number of copies: 6 / Formula: 3PE |
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Molecular weight | Theoretical: 748.065 Da |
Chemical component information | ![]() ChemComp-3PE: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40700 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |