+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10901 | |||||||||||||||
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Title | Vibrio mimicus PomA(5)B(2) complex | |||||||||||||||
Map data | Post Processed Vibrio mimicus PomAB complex volume | |||||||||||||||
Sample |
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Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Clostridium sporogenes (bacteria) / Vibrio mimicus (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 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_10901.map.gz | 85 MB | EMDB map data format | |
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Header (meta data) | emd-10901-v30.xml emd-10901.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10901_fsc.xml | 10.4 KB | Display | FSC data file |
Images | emd_10901.png | 223.7 KB | ||
Masks | emd_10901_msk_1.map | 91.1 MB | Mask map | |
Others | emd_10901_additional_1.map.gz emd_10901_additional_2.map.gz emd_10901_additional_3.map.gz emd_10901_additional_4.map.gz | 57.5 MB 70.6 MB 71.3 MB 71.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10901 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10901 | HTTPS FTP |
-Validation report
Summary document | emd_10901_validation.pdf.gz | 316.8 KB | Display | EMDB validaton report |
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Full document | emd_10901_full_validation.pdf.gz | 315.9 KB | Display | |
Data in XML | emd_10901_validation.xml.gz | 11.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10901 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10901 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10901.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Post Processed Vibrio mimicus PomAB complex volume | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_10901_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: relion local resolution Vibrio mimicus PomAB complex volume
File | emd_10901_additional_1.map | ||||||||||||
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Annotation | relion local resolution Vibrio mimicus PomAB complex volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: refinement volume
File | emd_10901_additional_2.map | ||||||||||||
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Annotation | refinement volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: half map 1
File | emd_10901_additional_3.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: half map 2
File | emd_10901_additional_4.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PomA(5)B(2)
Entire | Name: PomA(5)B(2) |
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Components |
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-Supramolecule #1: PomA(5)B(2)
Supramolecule | Name: PomA(5)B(2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Clostridium sporogenes (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: PomA
Macromolecule | Name: PomA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio mimicus (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDLATLIGLI GGLAFVIMAM VLGGSLMMFV DVVSILIVVG GSVFVVLMKF TMGQFFGAGK IASKAFMFK ADEPEDLIAK IVEMADAARK GGFLALEEME IPNPFMQKGI DLLVDGHDAD V VRATLQKD IALTDERHSK GTQVFRAFGD VAPAMGMIST LVGLVAMLSN ...String: MDLATLIGLI GGLAFVIMAM VLGGSLMMFV DVVSILIVVG GSVFVVLMKF TMGQFFGAGK IASKAFMFK ADEPEDLIAK IVEMADAARK GGFLALEEME IPNPFMQKGI DLLVDGHDAD V VRATLQKD IALTDERHSK GTQVFRAFGD VAPAMGMIST LVGLVAMLSN MDDPKSIGPA MA VALLTTL YGAVLSNMIF FPIADKLALR RDQETLNRRL IMDGVLAIQD GQNPRVIDSY LKN YLNASK RALDVDKE |
-Macromolecule #2: PomB
Macromolecule | Name: PomB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio mimicus (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDDEQQCKCP PPGLPAWLGT FADLMSLLMC FFVLLLSFSE MDVLKFKQIA GSMKFAFGVQ NRLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQQTIDI TQQTLDFQEG DSDRAGGNQR D SGKLTGGQ SAESSTQDNQ NTQSEMQQQQ AKAMSEQMET VAESIKKALS ...String: MDDEQQCKCP PPGLPAWLGT FADLMSLLMC FFVLLLSFSE MDVLKFKQIA GSMKFAFGVQ NRLEVKDIP KGTSIIAQEF RPGRPEPTPI DVIMQQTIDI TQQTLDFQEG DSDRAGGNQR D SGKLTGGQ SAESSTQDNQ NTQSEMQQQQ AKAMSEQMET VAESIKKALS REIEQGAIEV EN LGQQIDI RIREKGAFPE GSAFLQPKFR PLVRQIADLV KDIPGKVRVT GHTDNQKLDS ELY RSNWDL SAQRAVSVAQ EMEKVKGFDH QRLQVRGMAD TQPLGPNDTE AQRALNRRVE ISIL QGDPL YSDEVPSLGA PANQ |
-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 |