+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10897 | |||||||||||||||
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Title | Structure of ExbBD complex from pseudomonas savastonoi | |||||||||||||||
Map data | postprocesed pseudomonas savastanoi 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 | Pseudomonas savastanoi (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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_10897.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-10897-v30.xml emd-10897.xml | 21 KB 21 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10897_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_10897.png | 209 KB | ||
Masks | emd_10897_msk_1.map | 64 MB | Mask map | |
Others | emd_10897_additional_1.map.gz emd_10897_additional_2.map.gz emd_10897_half_map_1.map.gz emd_10897_half_map_2.map.gz | 41.4 MB 49.3 MB 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10897 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10897 | HTTPS FTP |
-Validation report
Summary document | emd_10897_validation.pdf.gz | 502.1 KB | Display | EMDB validaton report |
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Full document | emd_10897_full_validation.pdf.gz | 501.3 KB | Display | |
Data in XML | emd_10897_validation.xml.gz | 15 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10897 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10897 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10897.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocesed pseudomonas savastanoi 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_10897_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: relion local resolution filtered pseudomonas savastanoi ExbBD complex...
File | emd_10897_additional_1.map | ||||||||||||
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Annotation | relion local resolution filtered pseudomonas savastanoi ExbBD complex in LMNG | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: refinement volume pseudomonas savastanoi ExbBD complex in LMNG
File | emd_10897_additional_2.map | ||||||||||||
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Annotation | refinement volume pseudomonas savastanoi ExbBD complex in LMNG | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_10897_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_10897_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: Pseudomonas savastanoi (bacteria) |
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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Sequence | String: MTRIQSIASP TRMPRLPRAW RGVAALVLSL MFVPMALADQ SAPTAASAAP AAXATAPVVP DAAAPVQAM EPAAEDNSLG MAHDLSPWGM YQNAEVVVKA VMIGLAIASI ITWTIWISKG F ELLGAKRR LRGEIVNLKK ARSLNEASST ASKEGTLAHL LVHDALEEMR ...String: MTRIQSIASP TRMPRLPRAW RGVAALVLSL MFVPMALADQ SAPTAASAAP AAXATAPVVP DAAAPVQAM EPAAEDNSLG MAHDLSPWGM YQNAEVVVKA VMIGLAIASI ITWTIWISKG F ELLGAKRR LRGEIVNLKK ARSLNEASST ASKEGTLAHL LVHDALEEMR LSANSREREG IK ERVSFRL ERLVAACGRN MSMGTGVLAT IGSTAPFVGL FGTVWGIMNS FIGIAKTQTT NLA VVAPGI AEALLATALG LVAAIPAVVI YNVFARSIAG YKAQVSDASA HVLLLVSRDL DHLP EPTER NQQQPHMVKV G |
-Macromolecule #2: ExbD
Macromolecule | Name: ExbD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Sequence | String: MLVKPQRKHG PKAEMNVVPY IDVMLVLLVV FIVTAPLLTN AIPLDLPQTA ATAPLDDAKP VAISIDAKG GLFVDDQPLA EEQLPDALQN LHANDPDVAL TLRADTATDY GRVARVLADV Q RSGITRLA VITESL |
-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 |