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Yorodumi- EMDB-10899: Structure of the flagellar MotAB stator complex from Bacillus subtilis -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10899 | |||||||||||||||
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Title | Structure of the flagellar MotAB stator complex from Bacillus subtilis | |||||||||||||||
Map data | Bacillus subtilis MotAB complex volume post processed | |||||||||||||||
Sample |
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Keywords | Stator Flagellar rotation ion driven motor / MOTOR PROTEIN | |||||||||||||||
Function / homology | Function and homology information archaeal or bacterial-type flagellum-dependent cell motility / bacterial-type flagellum-dependent swarming motility / monoatomic ion transport / chemotaxis / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Bacillus subtilis (strain 168) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Lea SM / Deme JC | |||||||||||||||
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_10899.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-10899-v30.xml emd-10899.xml | 24.7 KB 24.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10899_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_10899.png | 243.4 KB | ||
Masks | emd_10899_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-10899.cif.gz | 5.9 KB | ||
Others | emd_10899_additional_1.map.gz emd_10899_additional_2.map.gz emd_10899_additional_3.map.gz emd_10899_half_map_1.map.gz emd_10899_half_map_2.map.gz | 41.1 MB 58.7 MB 49.3 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10899 | HTTPS FTP |
-Validation report
Summary document | emd_10899_validation.pdf.gz | 524.4 KB | Display | EMDB validaton report |
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Full document | emd_10899_full_validation.pdf.gz | 523.6 KB | Display | |
Data in XML | emd_10899_validation.xml.gz | 14.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10899 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10899 | HTTPS FTP |
-Related structure data
Related structure data | 6yslMC 6ysfC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10899.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacillus subtilis MotAB complex volume post processed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_10899_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Bacillus subtilis MotAB complex volume relion local resolution...
File | emd_10899_additional_1.map | ||||||||||||
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Annotation | Bacillus subtilis MotAB complex volume relion local resolution filtered | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Bacillus subtilis MotAB complex volume calculated from subset...
File | emd_10899_additional_2.map | ||||||||||||
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Annotation | Bacillus subtilis MotAB complex volume calculated from subset of particles with added fluo-OM | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Bacillus subtilis MotAB complex volume refinement volume
File | emd_10899_additional_3.map | ||||||||||||
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Annotation | Bacillus subtilis MotAB complex volume refinement volume | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Bacillus subtilis MotAB complex volume half map 1
File | emd_10899_half_map_1.map | ||||||||||||
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Annotation | Bacillus subtilis MotAB complex volume half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Bacillus subtilis MotAB complex volume half map 2
File | emd_10899_half_map_2.map | ||||||||||||
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Annotation | Bacillus subtilis MotAB complex volume half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : MotA(5)B(2)
Entire | Name: MotA(5)B(2) |
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Components |
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-Supramolecule #1: MotA(5)B(2)
Supramolecule | Name: MotA(5)B(2) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus subtilis (strain 168) (bacteria) |
-Macromolecule #1: Motility protein A
Macromolecule | Name: Motility protein A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (strain 168) (bacteria) |
Molecular weight | Theoretical: 29.370221 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDKTSLIGII LAFVALSVGM VLKGVSFSAL ANPAAILIII AGTISAVVIA FPTKEIKKVP TLFRVLFKEN KQLTIEELIP MFSEWAQLA RREGLLALEA SIEDVDDAFL KNGLSMAVDG QSAEFIRDIM TEEVEAMEDR HQAGAAIFTQ AGTYAPTLGV L GAVIGLIA ...String: MDKTSLIGII LAFVALSVGM VLKGVSFSAL ANPAAILIII AGTISAVVIA FPTKEIKKVP TLFRVLFKEN KQLTIEELIP MFSEWAQLA RREGLLALEA SIEDVDDAFL KNGLSMAVDG QSAEFIRDIM TEEVEAMEDR HQAGAAIFTQ AGTYAPTLGV L GAVIGLIA ALSHMDNTDE LGHAISAAFV ATLLGIFTGY VLWHPFANKL KRKSKQEVKL REVMIEGVLS VLEGQAPKVI EQ KLLMYLP AKDRLKFAEQ GEAQNGEKKE EEA UniProtKB: Motility protein A |
-Macromolecule #2: Motility protein B
Macromolecule | Name: Motility protein B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (strain 168) (bacteria) |
Molecular weight | Theoretical: 29.529768 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARKKKKKHE DEHVDESWLV PYADILTLLL ALFIVLYASS SIDAAKFQML SKSFNEVFTG GTGVLDYSSV TPPENESDGI DEVKKEKEE KEKNKKEKEK AADQEELENV KSQVEKFIKD KKLEHQLETK MTSEGLLITI KDSIFFDSGK ATIRKEDVPL A KEISNLLV ...String: MARKKKKKHE DEHVDESWLV PYADILTLLL ALFIVLYASS SIDAAKFQML SKSFNEVFTG GTGVLDYSSV TPPENESDGI DEVKKEKEE KEKNKKEKEK AADQEELENV KSQVEKFIKD KKLEHQLETK MTSEGLLITI KDSIFFDSGK ATIRKEDVPL A KEISNLLV INPPRNIIIS GHTDNMPIKN SEFQSNWHLS VMRAVNFMGL LIENPKLDAK VFSAKGYGEY KPVASNKTAE GR SKNRRVE VLILPRGAAE TNEK UniProtKB: Motility protein B |
-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 |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-6ysl: |