+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10902 | |||||||||||||||
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Title | Escherichia coli ExbB(5)D(2) complex | |||||||||||||||
Map data | postprocessed volume ExbBD complex in LMNG | |||||||||||||||
Sample |
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Function / homology | Function and homology information transmembrane transporter activity / protein transport / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||||||||
Authors | Lea SM / Deme JC / Johnson S | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structures of the stator complex that drives rotation of the bacterial flagellum. Authors: Justin C Deme / Steven Johnson / Owen Vickery / Amy Aron / Holly Monkhouse / Thomas Griffiths / Rory Hennell James / Ben C Berks / James W Coulton / Phillip J Stansfeld / Susan M Lea / Abstract: The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor ...The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor surrounded by stator units that couple ion flow across the cytoplasmic membrane to generate torque. Here, we present the structures of the stator complexes from Clostridium sporogenes, Bacillus subtilis and Vibrio mimicus, allowing interpretation of the extensive body of data on stator mechanism. The structures reveal an unexpected asymmetric AB subunit assembly where the five A subunits enclose the two B subunits. Comparison to structures of other ion-driven motors indicates that this AB architecture is fundamental to bacterial systems that couple energy from ion flow to generate mechanical work at a distance and suggests that such events involve rotation in the motor structures. | |||||||||||||||
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_10902.map.gz | 58.8 MB | EMDB map data format | |
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Header (meta data) | emd-10902-v30.xml emd-10902.xml | 22.4 KB 22.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10902_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_10902.png | 154.8 KB | ||
Masks | emd_10902_msk_1.map | 64 MB | Mask map | |
Others | emd_10902_additional_1.map.gz emd_10902_additional_2.map.gz emd_10902_half_map_1.map.gz emd_10902_half_map_2.map.gz | 41.1 MB 48.7 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10902 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10902 | HTTPS FTP |
-Validation report
Summary document | emd_10902_validation.pdf.gz | 455.2 KB | Display | EMDB validaton report |
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Full document | emd_10902_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | emd_10902_validation.xml.gz | 14.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10902 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10902 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10902.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocessed volume ExbBD complex in LMNG | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.822 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10902_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: relion local resolution volume
File | emd_10902_additional_1.map | ||||||||||||
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Annotation | relion local resolution volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: refinement volume
File | emd_10902_additional_2.map | ||||||||||||
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Annotation | refinement volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_10902_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_10902_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ExbB(5)D(2)
Entire | Name: ExbB(5)D(2) |
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Components |
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-Supramolecule #1: ExbB(5)D(2)
Supramolecule | Name: ExbB(5)D(2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 195 KDa |
-Macromolecule #1: ExbB
Macromolecule | Name: ExbB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLN QANDIAADFG SKSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV A AVGRQMGR GNGYLATIGA ISPFVGLFGT VWGIMNSFIG IAQTQTTNLA ...String: MGNNLMQTDL SVWGMYQHAD IVVKCVMIGL ILASVVTWAI FFSKSVEFFN QKRRLKREQQ LLAEARSLN QANDIAADFG SKSLSLHLLN EAQNELELSE GSDDNEGIKE RTSFRLERRV A AVGRQMGR GNGYLATIGA ISPFVGLFGT VWGIMNSFIG IAQTQTTNLA VVAPGIAEAL LA TAIGLVA AIPAVVIYNV FARQIGGFKA MLGDVAAQVL LLQSRDLDLE ASAAAHPVRV AQK LRAG |
-Macromolecule #2: ExbD
Macromolecule | Name: ExbD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAMHLNENLD DNGEMHDINV TPFIDVMLVL LIIFMVAAPL ATVDVKVNLP ASTSTPQPRP EKPVYLSVK ADNSMFIGND PVTDETMITA LNALTEGKKD TTIFFRADKT VDYETLMKVM D TLHQAGYL KIGLVGEETA KAK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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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: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0003 µm / Nominal defocus min: 0.0001 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |