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Yorodumi- EMDB-21897: The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21897 | |||||||||
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Title | The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ubiquinol oxidase cytochrome bo3 / membrane protein / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / 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 ...cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / 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 / respiratory electron transport chain / aerobic respiration / membrane => GO:0016020 / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.38 Å | |||||||||
Authors | Su C-C | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Methods / Year: 2021 Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu / Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21897.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-21897-v30.xml emd-21897.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_21897.png | 140.8 KB | ||
Filedesc metadata | emd-21897.cif.gz | 6.6 KB | ||
Others | emd_21897_additional_1.map.gz | 97.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21897 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21897 | HTTPS FTP |
-Validation report
Summary document | emd_21897_validation.pdf.gz | 523.4 KB | Display | EMDB validaton report |
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Full document | emd_21897_full_validation.pdf.gz | 523 KB | Display | |
Data in XML | emd_21897_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_21897_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21897 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21897 | HTTPS FTP |
-Related structure data
Related structure data | 6wtiMC 6wtzC 6wu0C 6wu6C 7jz2C 7jz3C 7jz6C 7jzhC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21897.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_21897_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : ubiquinol oxidase
+Supramolecule #1: ubiquinol oxidase
+Macromolecule #1: Cytochrome o ubiquinol oxidase, subunit I
+Macromolecule #2: Ubiquinol oxidase subunit 2
+Macromolecule #3: Cytochrome o ubiquinol oxidase
+Macromolecule #4: Cytochrome o ubiquinol oxidase, subunit IV
+Macromolecule #5: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #6: HEME O
+Macromolecule #7: COPPER (II) ION
+Macromolecule #8: Ubiquinone-8
+Macromolecule #9: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #10: pentadecyl(tetradecyl)peroxyanhydride
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 334222 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |