+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22528 | |||||||||
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Title | Succinate: quinone oxidoreductase SQR from E.coli K12 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Complex / Succinate: quinone oxidoreductase / SdhA / sdhB / SdhC / SdhD / ELECTRON TRANSPORT / ELECTRON TRANSPORT-OXIDOREDUCTASE complex | |||||||||
Function / homology | Function and homology information : / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...: / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / respiratory electron transport chain / aerobic respiration / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.5 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_22528.map.gz | 9.6 MB | EMDB map data format | |
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Header (meta data) | emd-22528-v30.xml emd-22528.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
Images | emd_22528.png | 279 KB | ||
Filedesc metadata | emd-22528.cif.gz | 6.1 KB | ||
Others | emd_22528_additional_1.map.gz | 154.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22528 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22528 | HTTPS FTP |
-Validation report
Summary document | emd_22528_validation.pdf.gz | 537 KB | Display | EMDB validaton report |
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Full document | emd_22528_full_validation.pdf.gz | 536.6 KB | Display | |
Data in XML | emd_22528_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | emd_22528_validation.cif.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22528 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22528 | HTTPS FTP |
-Related structure data
Related structure data | 7jz2MC 6wtiC 6wtzC 6wu0C 6wu6C 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_22528.map.gz / Format: CCP4 / Size: 10.2 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_22528_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Succinate: quinone oxidoreductase SQR from E.coli K12
+Supramolecule #1: Succinate: quinone oxidoreductase SQR from E.coli K12
+Macromolecule #1: Succinate dehydrogenase flavoprotein subunit
+Macromolecule #2: Succinate dehydrogenase iron-sulfur subunit
+Macromolecule #3: Succinate dehydrogenase cytochrome b556 subunit
+Macromolecule #4: Succinate dehydrogenase hydrophobic membrane anchor subunit
+Macromolecule #5: FLAVIN-ADENINE DINUCLEOTIDE
+Macromolecule #6: SODIUM ION
+Macromolecule #7: FE2/S2 (INORGANIC) CLUSTER
+Macromolecule #8: IRON/SULFUR CLUSTER
+Macromolecule #9: FE3-S4 CLUSTER
+Macromolecule #10: 1,2-Distearoyl-sn-glycerophosphoethanolamine
+Macromolecule #11: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #12: UBIQUINONE-2
-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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38471 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |