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- EMDB-22225: R. capsulatus cyt bc1 with one FeS protein in b position and one ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22225 | |||||||||||||||||||||||||||
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Title | R. capsulatus cyt bc1 with one FeS protein in b position and one in c position (CIII2 b-c) | |||||||||||||||||||||||||||
![]() | R. capsulatus cyt bc1 with one FeS protein in b-position and one in c-position (CIII2-bc) | |||||||||||||||||||||||||||
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Function / homology | ![]() respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / : / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||||||||||||||
![]() | Steimle S / Van Eeuwen T / Ozturk Y / Kim HJ / Braitbard M / Selamoglu N / Garcia BA / Schneidman-Duhovny D / Murakami K / Daldal F | |||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cryo-EM structures of engineered active bc-cbb type CIIICIV super-complexes and electronic communication between the complexes. Authors: Stefan Steimle / Trevor van Eeuwen / Yavuz Ozturk / Hee Jong Kim / Merav Braitbard / Nur Selamoglu / Benjamin A Garcia / Dina Schneidman-Duhovny / Kenji Murakami / Fevzi Daldal / ![]() ![]() ![]() Abstract: Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc (Complex ...Respiratory electron transport complexes are organized as individual entities or combined as large supercomplexes (SC). Gram-negative bacteria deploy a mitochondrial-like cytochrome (cyt) bc (Complex III, CIII), and may have specific cbb-type cyt c oxidases (Complex IV, CIV) instead of the canonical aa-type CIV. Electron transfer between these complexes is mediated by soluble (c) and membrane-anchored (c) cyts. Here, we report the structure of an engineered bc-cbb type SC (CIIICIV, 5.2 Å resolution) and three conformers of native CIII (3.3 Å resolution). The SC is active in vivo and in vitro, contains all catalytic subunits and cofactors, and two extra transmembrane helices attributed to cyt c and the assembly factor CcoH. The cyt c is integral to SC, its cyt domain is mobile and it conveys electrons to CIV differently than cyt c. The successful production of a native-like functional SC and determination of its structure illustrate the characteristics of membrane-confined and membrane-external respiratory electron transport pathways in Gram-negative bacteria. | |||||||||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 235.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xkuMC ![]() 6xi0C ![]() 6xktC ![]() 6xkvC ![]() 6xkwC ![]() 6xkxC ![]() 6xkzC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 35.8 TB Data #1: tripartite SC - dataset 1 [micrographs - multiframe] Data #2: tripartite SC - dataset 2 [micrographs - multiframe] Data #3: tripartite SC - dataset 3 [micrographs - multiframe] Data #4: tripartite SC - dataset 4 [micrographs - multiframe] Data #5: tripartite SC - dataset 5 [micrographs - multiframe] Data #6: tripartite SC - dataset 6 [micrographs - multiframe] Data #7: tripartite SC - dataset 7 [micrographs - multiframe] Data #8: bipartite SC - dataset 1 [micrographs - single frame] Data #9: bipartite SC - dataset 2 [micrographs - multiframe] Data #10: bipartite SC - dataset 3 [micrographs - multiframe]) |
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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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Annotation | R. capsulatus cyt bc1 with one FeS protein in b-position and one in c-position (CIII2-bc) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : ubiquinol:cytochrome c reductase (complex III or cyt bc1 complex)
Entire | Name: ubiquinol:cytochrome c reductase (complex III or cyt bc1 complex) |
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Components |
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-Supramolecule #1: ubiquinol:cytochrome c reductase (complex III or cyt bc1 complex)
Supramolecule | Name: ubiquinol:cytochrome c reductase (complex III or cyt bc1 complex) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Ubiquinol-cytochrome c reductase iron-sulfur subunit
Macromolecule | Name: Ubiquinol-cytochrome c reductase iron-sulfur subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: quinol-cytochrome-c reductase |
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Source (natural) | Organism: ![]() Strain: ATCC BAA-309 / NBRC 16581 / SB1003 |
Molecular weight | Theoretical: 20.465109 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSHAEDNAGT RRDFLYHATA ATGVVVTGAA VWPLINQMNA SADVKAMASI FVDVSAVEVG TQLTVKWRGK PVFIRRRDEK DIELARSVP LGALRDTSAE NANKPGAEAT DENRTLPAFD GTNTGEWLVM LGVCTHLGCV PMGDKSGDFG GWFCPCHGSH Y DSAGRIRK GPAPRNLDIP VAAFVDETTI KLG |
-Macromolecule #2: Cytochrome b
Macromolecule | Name: Cytochrome b / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC BAA-309 / NBRC 16581 / SB1003 |
Molecular weight | Theoretical: 49.386469 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSGIPHDHYE PKTGIEKWLH DRLPIVGLVY DTIMIPTPKN LNWWWIWGIV LAFTLVLQIV TGIVLAMHYT PHVDLAFASV EHIMRDVNG GWAMRYIHAN GASLFFLAVY IHIFRGLYYG SYKAPREITW IVGMVIYLLM MGTAFMGYVL PWGQMSFWGA T VITGLFGA ...String: MSGIPHDHYE PKTGIEKWLH DRLPIVGLVY DTIMIPTPKN LNWWWIWGIV LAFTLVLQIV TGIVLAMHYT PHVDLAFASV EHIMRDVNG GWAMRYIHAN GASLFFLAVY IHIFRGLYYG SYKAPREITW IVGMVIYLLM MGTAFMGYVL PWGQMSFWGA T VITGLFGA IPGIGPSIQA WLLGGPAVDN ATLNRFFSLH YLLPFVIAAL VAIHIWAFHT TGNNNPTGVE VRRTSKADAE KD TLPFWPY FVIKDLFALA LVLLGFFAVV AYMPNYLGHP DNYVQANPLS TPAHIVPEWY FLPFYAILRA FAADVWVVIL VDG LTFGIV DAKFFGVIAM FGAIAVMALA PWLDTSKVRS GAYRPKFRMW FWFLVLDFVV LTWVGAMPTE YPYDWISLIA STYW FAYFL VILPLLGATE KPEPIPASIE EDFNSHYGNP AE |
-Macromolecule #3: Cytochrome c1
Macromolecule | Name: Cytochrome c1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: ATCC BAA-309 / NBRC 16581 / SB1003 |
Molecular weight | Theoretical: 30.352615 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKKLLISAVS ALVLGSGAAF ANSNVPDHAF SFEGIFGKYD QAQLRRGFQV YNEVCSACHG MKFVPIRTLA DDGGPQLDPT FVREYAAGL DTIIDKDSGE ERDRKETDMF PTRVGDGMGP DLSVMAKARA GFSGPAGSGM NQLFKGMGGP EYIYNYVIGF E ENPECAPE ...String: MKKLLISAVS ALVLGSGAAF ANSNVPDHAF SFEGIFGKYD QAQLRRGFQV YNEVCSACHG MKFVPIRTLA DDGGPQLDPT FVREYAAGL DTIIDKDSGE ERDRKETDMF PTRVGDGMGP DLSVMAKARA GFSGPAGSGM NQLFKGMGGP EYIYNYVIGF E ENPECAPE GIDGYYYNKT FQIGGVPDTC KDAAGVKITH GSWARMPPPL VDDQVTYEDG TPATVDQMAQ DVSAFLMWAA EP KLVARKQ MGLVAMVMLG LLSVMLYLTN KRLWAPYKGH KA |
-Macromolecule #4: FE2/S2 (INORGANIC) CLUSTER
Macromolecule | Name: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: FES |
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Molecular weight | Theoretical: 175.82 Da |
Chemical component information | ![]() ChemComp-FES: |
-Macromolecule #5: HEME C
Macromolecule | Name: HEME C / type: ligand / ID: 5 / Number of copies: 6 / Formula: HEC |
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Molecular weight | Theoretical: 618.503 Da |
Chemical component information | ![]() ChemComp-HEC: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
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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: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |