+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20583 | |||||||||
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Title | ExbB-ExbD complex in MSP1E3D1 nanodisc | |||||||||
Map data | ExbB-ExbD complex in MSP1E3D1 nanodisc | |||||||||
Sample |
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Keywords | molecular motor / Ton system / membrane protein / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane ...ferrichrome import into cell / energy transducer activity / bacteriocin transport / cobalamin transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / protein import / transmembrane transporter activity / transmembrane transporter complex / cell outer membrane / protein transport / intracellular iron ion homeostasis / protein stabilization / protein homodimerization activity / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Celia H / Botos I | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2019 Title: Cryo-EM structure of the bacterial Ton motor subcomplex ExbB-ExbD provides information on structure and stoichiometry. Authors: Herve Celia / Istvan Botos / Xiaodan Ni / Tara Fox / Natalia De Val / Roland Lloubes / Jiansen Jiang / Susan K Buchanan / Abstract: The TonB-ExbB-ExbD molecular motor harnesses the proton motive force across the bacterial inner membrane to couple energy to transporters at the outer membrane, facilitating uptake of essential ...The TonB-ExbB-ExbD molecular motor harnesses the proton motive force across the bacterial inner membrane to couple energy to transporters at the outer membrane, facilitating uptake of essential nutrients such as iron and cobalamine. TonB physically interacts with the nutrient-loaded transporter to exert a force that opens an import pathway across the outer membrane. Until recently, no high-resolution structural information was available for this unique molecular motor. We published the first crystal structure of ExbB-ExbD in 2016 and showed that five copies of ExbB are arranged as a pentamer around a single copy of ExbD. However, our spectroscopic experiments clearly indicated that two copies of ExbD are present in the complex. To resolve this ambiguity, we used single-particle cryo-electron microscopy to show that the ExbB pentamer encloses a dimer of ExbD in its transmembrane pore, and not a monomer as previously reported. The revised stoichiometry has implications for motor function. | |||||||||
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_20583.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-20583-v30.xml emd-20583.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_20583.png | 123 KB | ||
Filedesc metadata | emd-20583.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20583 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20583 | HTTPS FTP |
-Validation report
Summary document | emd_20583_validation.pdf.gz | 376.1 KB | Display | EMDB validaton report |
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Full document | emd_20583_full_validation.pdf.gz | 375.7 KB | Display | |
Data in XML | emd_20583_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_20583_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20583 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20583 | HTTPS FTP |
-Related structure data
Related structure data | 6tyiMC 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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-Map
File | Download / File: emd_20583.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ExbB-ExbD complex in MSP1E3D1 nanodisc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ton subcomplex ExbB-ExbD reconstituted in lipid nanodisc
Entire | Name: Ton subcomplex ExbB-ExbD reconstituted in lipid nanodisc |
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Components |
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-Supramolecule #1: Ton subcomplex ExbB-ExbD reconstituted in lipid nanodisc
Supramolecule | Name: Ton subcomplex ExbB-ExbD reconstituted in lipid nanodisc type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
-Macromolecule #1: Biopolymer transport protein ExbB
Macromolecule | Name: Biopolymer transport protein ExbB / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 26.312322 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLNQ ANDIAADFGS KSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV AAVGRQMGRG NGYLATIGAI SPFVGLFGTV WGIMNSFIGI A QTQTTNLA ...String: MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLNQ ANDIAADFGS KSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV AAVGRQMGRG NGYLATIGAI SPFVGLFGTV WGIMNSFIGI A QTQTTNLA VVAPGIAEAL LATAIGLVAA IPAVVIYNVF ARQIGGFKAM LGDVAAQVLL LQSRDLDLEA SAAAHPVRVA QK LRAG UniProtKB: Biopolymer transport protein ExbB |
-Macromolecule #2: Biopolymer transport protein ExbD
Macromolecule | Name: Biopolymer transport protein ExbD / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 18.161674 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MAMHLNENLD DNGEMHDINV TPFIDVMLVL LIIFMVAAPL ATVDVKVNLP ASTSTPQPRP EKPVYLSVKA DNSMFIGNDP VTDETMITA LNALTEGKKD TTIFFRADKT VDYETLMKVM DTLHQAGYLK IGLVGEETAK AKENLYFQGN AGSGHHHHHH H HHH UniProtKB: Biopolymer transport protein ExbD |
-Macromolecule #3: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
Macromolecule | Name: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE type: ligand / ID: 3 / Number of copies: 1 / Formula: PGT |
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Molecular weight | Theoretical: 751.023 Da |
Chemical component information | ChemComp-PGT: |
-Macromolecule #4: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...
Macromolecule | Name: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE type: ligand / ID: 4 / Number of copies: 3 / Formula: PEV |
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Molecular weight | Theoretical: 720.012 Da |
Chemical component information | ChemComp-PEV: |
-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 K2 SUMMIT (4k x 4k) / Average electron dose: 1.6 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: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85936 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |