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Yorodumi- EMDB-10895: Structure of the flagellar MotAB stator complex from Clostridium ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10895 | |||||||||||||||
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Title | Structure of the flagellar MotAB stator complex from Clostridium sporogenes | |||||||||||||||
Map data | post processed volume MotAB complex clostridium sporogenes | |||||||||||||||
Sample |
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Keywords | Stator Flagellar rotation ion driven motor / MOTOR PROTEIN | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Clostridium sporogenes (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_10895.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-10895-v30.xml emd-10895.xml | 22.1 KB 22.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10895_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_10895.png | 235.3 KB | ||
Masks | emd_10895_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-10895.cif.gz | 5.9 KB | ||
Others | emd_10895_additional_1.map.gz emd_10895_additional_2.map.gz emd_10895_half_map_1.map.gz emd_10895_half_map_2.map.gz | 41.3 MB 49.1 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10895 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10895 | HTTPS FTP |
-Validation report
Summary document | emd_10895_validation.pdf.gz | 972 KB | Display | EMDB validaton report |
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Full document | emd_10895_full_validation.pdf.gz | 971.6 KB | Display | |
Data in XML | emd_10895_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_10895_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10895 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10895 | HTTPS FTP |
-Related structure data
Related structure data | 6ysfMC 6yslC 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_10895.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | post processed volume MotAB complex clostridium sporogenes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_10895_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Relion Local Resolution filtered volume MotAB clostridium sporogenes
File | emd_10895_additional_1.map | ||||||||||||
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Annotation | Relion Local Resolution filtered volume MotAB clostridium sporogenes | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Refinement volume MotAB clostridium sporogenes
File | emd_10895_additional_2.map | ||||||||||||
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Annotation | Refinement volume MotAB clostridium sporogenes | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_10895_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_10895_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : MotAB
Entire | Name: MotAB |
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Components |
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-Supramolecule #1: MotAB
Supramolecule | Name: MotAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Clostridium sporogenes (bacteria) |
-Macromolecule #1: Chemotaxis motB protein
Macromolecule | Name: Chemotaxis motB protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium sporogenes (bacteria) |
Molecular weight | Theoretical: 27.948547 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARRNKKGGG GDEIRGDEWL ATFSDTITLL LTFFILLYSF SSVDAQKFQQ VASAMQVAMT GQSGNTIVDY NLKNGDVPLV GETTKLGRE TGSDAKSDSK EVYNEVNKFV DKNNLKSSVE VKEDGRGVII QLRDNVLFEI GRADIKPQSK QIMDKINGLI A TLPNEVIV ...String: MARRNKKGGG GDEIRGDEWL ATFSDTITLL LTFFILLYSF SSVDAQKFQQ VASAMQVAMT GQSGNTIVDY NLKNGDVPLV GETTKLGRE TGSDAKSDSK EVYNEVNKFV DKNNLKSSVE VKEDGRGVII QLRDNVLFEI GRADIKPQSK QIMDKINGLI A TLPNEVIV EGHTDNVPIK NEVYGSNWEL STARAVNVLR YFVETKKQNP VRFTAAGYGE YRPIAQNNSD VNKAKNRRVN IV IVSKEKE SSKK UniProtKB: Chemotaxis protein MotB |
-Macromolecule #2: Chemotaxis MotA protein
Macromolecule | Name: Chemotaxis MotA protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium sporogenes (bacteria) |
Molecular weight | Theoretical: 29.613506 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKRDILTPI GFVLCFGLVL WGMASGGSNL KVFWDVASVF ITIGGSMAAM LITYPMDEFK RLLIVIRQTF KDNGMSNIDV IQNFVDLSR KARREGLLSL EDAINNLTDD YMKKGLRMVV DGIEPETIRE IMELEIDEME KRHKSGADML KTWGGYAPAF G MVGTLIGL ...String: MKKRDILTPI GFVLCFGLVL WGMASGGSNL KVFWDVASVF ITIGGSMAAM LITYPMDEFK RLLIVIRQTF KDNGMSNIDV IQNFVDLSR KARREGLLSL EDAINNLTDD YMKKGLRMVV DGIEPETIRE IMELEIDEME KRHKSGADML KTWGGYAPAF G MVGTLIGL IQMLANLTDS STIASGMGKA LITTFYGSLM ANAVFNPMGA NLMFKSGVEA TTREMVLEGV LAIQSGVNPR IM EEKLVSY LSPPERQAYS KVQVSGEGAA QNG UniProtKB: Chemotaxis MotA protein |
-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-6ysf: |