+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21906 | |||||||||
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Title | succinate-coenzyme Q reductase | |||||||||
Map data | succinate-coenzyme Q reductase | |||||||||
Sample |
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Keywords | Complex / succinate-coenzyme Q reductase / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / ubiquinone binding / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / ubiquinone binding / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / electron transport chain / aerobic respiration / tricarboxylic acid cycle / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli 908573 (bacteria) / Escherichia coli (strain SE11) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Lyu M / 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_21906.map.gz | 10.5 MB | EMDB map data format | |
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Header (meta data) | emd-21906-v30.xml emd-21906.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_21906.png | 263.3 KB | ||
Filedesc metadata | emd-21906.cif.gz | 6.2 KB | ||
Others | emd_21906_additional_1.map.gz | 97.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21906 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21906 | HTTPS FTP |
-Related structure data
Related structure data | 6wu6MC 6wtiC 6wtzC 6wu0C 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_21906.map.gz / Format: CCP4 / Size: 11.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | succinate-coenzyme Q reductase | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: succinate-coenzyme Q reductase
File | emd_21906_additional_1.map | ||||||||||||
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Annotation | succinate-coenzyme Q reductase | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : succinate-coenzyme Q reductase complex
+Supramolecule #1: succinate-coenzyme Q reductase complex
+Macromolecule #1: Succinate dehydrogenase iron-sulfur subunit
+Macromolecule #2: Succinate dehydrogenase
+Macromolecule #3: Succinate dehydrogenase hydrophobic membrane anchor subunit
+Macromolecule #4: Succinate dehydrogenase flavoprotein subunit
+Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #6: IRON/SULFUR CLUSTER
+Macromolecule #7: FE3-S4 CLUSTER
+Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #9: FLAVIN-ADENINE DINUCLEOTIDE
+Macromolecule #10: SODIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12706 |