+Open data
-Basic information
Entry | Database: PDB / ID: 6wu6 | ||||||
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Title | succinate-coenzyme Q reductase | ||||||
Components |
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Keywords | ELECTRON TRANSPORT / Complex / succinate-coenzyme Q reductase | ||||||
Function / homology | Function and homology information : / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / 3 iron, 4 sulfur cluster binding / ubiquinone binding / iron-sulfur cluster binding / tricarboxylic acid cycle ...: / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / 3 iron, 4 sulfur cluster binding / ubiquinone binding / iron-sulfur cluster binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / membrane => GO:0016020 / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Escherichia coli 908573 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Lyu, M. / Su, C.-C. / Morgan, C.E. / Yu, E.W. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wu6.cif.gz | 485.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wu6.ent.gz | 399.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wu6_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6wu6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6wu6_validation.xml.gz | 88.2 KB | Display | |
Data in CIF | 6wu6_validation.cif.gz | 128.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/6wu6 ftp://data.pdbj.org/pub/pdb/validation_reports/wu/6wu6 | HTTPS FTP |
-Related structure data
Related structure data | 21906MC 6wtiC 6wtzC 6wu0C 7jz2C 7jz3C 7jz6C 7jzhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Succinate dehydrogenase ... , 3 types, 9 molecules BFJDHLAEI
#1: Protein | Mass: 26800.912 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sdhB / Production host: Escherichia coli (E. coli) References: UniProt: A0A037Y3E8, UniProt: P07014*PLUS, succinate dehydrogenase #3: Protein | Mass: 12874.438 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli 908573 (bacteria) / Gene: HMPREF1611_01928 / Production host: Escherichia coli (E. coli) / References: UniProt: V0YWY6 #4: Protein | Mass: 64502.766 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain SE11) (bacteria) Strain: SE11 / Gene: ECSE_0783 / Production host: Escherichia coli (E. coli) / References: UniProt: B6I7Z5, succinate dehydrogenase |
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-Protein , 1 types, 3 molecules CGK
#2: Protein | Mass: 14313.100 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sdhC, cybA, dhsC / Production host: Escherichia coli (E. coli) References: UniProt: C3TIP7, UniProt: P69054*PLUS, succinate dehydrogenase |
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-Non-polymers , 6 types, 18 molecules
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: succinate-coenzyme Q reductase complex / Type: COMPLEX / Entity ID: #4 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12706 / Symmetry type: POINT |