[English] 日本語
Yorodumi- EMDB-42387: Cryo-EM structure of a single subunit of a Clockwise-locked form ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42387 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a single subunit of a Clockwise-locked form of the Salmonella enterica Typhimurium flagellar C-ring. | |||||||||||||||
Map data | structure of a single subunit of a Clockwise-locked form of the Salmonella enterica Typhimurium flagellar C-ring. | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | Flagella / C-ring / motor / rotation / MOTOR PROTEIN | |||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / positive chemotaxis / cytoskeletal motor activity / bacterial-type flagellum-dependent cell motility / chemotaxis / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||||||||
Authors | Johnson S / Deme JC / Lea SM | |||||||||||||||
Funding support | United States, United Kingdom, 4 items
| |||||||||||||||
Citation | Journal: Nat Microbiol / Year: 2024 Title: Structural basis of directional switching by the bacterial flagellum. Authors: Steven Johnson / Justin C Deme / Emily J Furlong / Joseph J E Caesar / Fabienne F V Chevance / Kelly T Hughes / Susan M Lea / Abstract: The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar ...The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotAB stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum. | |||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_42387.map.gz | 255 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-42387-v30.xml emd-42387.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42387_fsc.xml | 19 KB | Display | FSC data file |
Images | emd_42387.png | 121.9 KB | ||
Masks | emd_42387_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-42387.cif.gz | 6.3 KB | ||
Others | emd_42387_additional_1.map.gz emd_42387_additional_2.map.gz emd_42387_half_map_1.map.gz emd_42387_half_map_2.map.gz | 482.9 MB 2.9 MB 474.4 MB 474.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42387 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42387 | HTTPS FTP |
-Validation report
Summary document | emd_42387_validation.pdf.gz | 859.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_42387_full_validation.pdf.gz | 858.8 KB | Display | |
Data in XML | emd_42387_validation.xml.gz | 26 KB | Display | |
Data in CIF | emd_42387_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42387 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42387 | HTTPS FTP |
-Related structure data
Related structure data | 8umxMC 8ucsC 8umdC 8uoxC 8uplC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_42387.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | structure of a single subunit of a Clockwise-locked form of the Salmonella enterica Typhimurium flagellar C-ring. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.664 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_42387_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: #1
File | emd_42387_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: DeepEMhancer map
File | emd_42387_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | DeepEMhancer map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map B
File | emd_42387_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map A
File | emd_42387_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Intact flagellar basal body with C-ring locked in the clockwise c...
Entire | Name: Intact flagellar basal body with C-ring locked in the clockwise conformation |
---|---|
Components |
|
-Supramolecule #1: Intact flagellar basal body with C-ring locked in the clockwise c...
Supramolecule | Name: Intact flagellar basal body with C-ring locked in the clockwise conformation type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Residues 169-171 of FliG have been deleted on the chromosome. |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Macromolecule #1: Flagellar M-ring protein
Macromolecule | Name: Flagellar M-ring protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 61.295645 KDa |
Sequence | String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE ...String: MSATASTATQ PKPLEWLNRL RANPRIPLIV AGSAAVAIVV AMVLWAKTPD YRTLFSNLSD QDGGAIVAQL TQMNIPYRFA NGSGAIEVP ADKVHELRLR LAQQGLPKGG AVGFELLDQE KFGISQFSEQ VNYQRALEGE LARTIETLGP VKSARVHLAM P KPSLFVRE QKSPSASVTV TLEPGRALDE GQISAVVHLV SSAVAGLPPG NVTLVDQSGH LLTQSNTSGR DLNDAQLKFA ND VESRIQR RIEAILSPIV GNGNVHAQVT AQLDFANKEQ TEEHYSPNGD ASKATLRSRQ LNISEQVGAG YPGGVPGALS NQP APPNEA PIATPPTNQQ NAQNTPQTST STNSNSAGPR STQRNETSNY EVDRTIRHTK MNVGDIERLS VAVVVNYKTL ADGK PLPLT ADQMKQIEDL TREAMGFSDK RGDTLNVVNS PFSAVDNTGG ELPFWQQQSF IDQLLAAGRW LLVLVVAWIL WRKAV RPQL TRRVEEAKAA QEQAQVRQET EEAVEVRLSK DEQLQQRRAN QRLGAEVMSQ RIREMSDNDP RVVALVIRQW MSNDHE UniProtKB: Flagellar M-ring protein |
-Macromolecule #2: Flagellar motor switch protein FliG
Macromolecule | Name: Flagellar motor switch protein FliG / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 36.651688 KDa |
Sequence | String: MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ ...String: MSNLSGTDKS VILLMTIGED RAAEVFKHLS TREVQALSTA MANVRQISNK QLTDVLSEFE QEAEQFAALN INANEYLRSV LVKALGEER ASSLLEDILE TRDTTSGIET LNFMEPQSAA DLIRDEHPQI IATILVHLKR SQAADILALF DERLRHDVML R IATFGGVQ LAELTEVLNG LLDGQNLKRS KMGGVRTAAE IINLMKTQQE EAVITAVREF DGELAQKIID EMFLFENLVD VD DRSIQRL LQEVDSESLL IALKGAEPPL REKFLRNMSQ RAADILRDDL ANRGPVRLSQ VENEQKAILL IVRRLAETGE MVI GSGEDT YV UniProtKB: Flagellar motor switch protein FliG |
-Macromolecule #3: Flagellar motor switch protein FliM
Macromolecule | Name: Flagellar motor switch protein FliM / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 37.901066 KDa |
Sequence | String: MGDSILSQAE IDALLNGDSD TKDEPTPGIA SDSDIRPYDP NTQRRVVRER LQALEIINER FARQFRMGLF NLLRRSPDIT VGAIRIQPY HEFARNLPVP TNLNLIHLKP LRGTGLVVFS PSLVFIAVDN LFGGDGRFPT KVEGREFTHT EQRVINRMLK L ALEGYSDA ...String: MGDSILSQAE IDALLNGDSD TKDEPTPGIA SDSDIRPYDP NTQRRVVRER LQALEIINER FARQFRMGLF NLLRRSPDIT VGAIRIQPY HEFARNLPVP TNLNLIHLKP LRGTGLVVFS PSLVFIAVDN LFGGDGRFPT KVEGREFTHT EQRVINRMLK L ALEGYSDA WKAINPLEVE YVRSEMQVKF TNITTSPNDI VVNTPFHVEI GNLTGEFNIC LPFSMIEPLR ELLVNPPLEN SR HEDQNWR DNLVRQVQHS ELELVANFAD IPLRLSQILK LKPGDVLPIE KPDRIIAHVD GVPVLTSQYG TVNGQYALRV EHL INPILN SLNEEQPK UniProtKB: Flagellar motor switch protein FliM |
-Macromolecule #4: Flagellar motor switch protein FliN
Macromolecule | Name: Flagellar motor switch protein FliN / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Molecular weight | Theoretical: 14.801823 KDa |
Sequence | String: MSDMNNPSDE NTGALDDLWA DALNEQKATT TKSAADAVFQ QLGGGDVSGA MQDIDLIMDI PVKLTVELGR TRMTIKELLR LTQGSVVAL DGLAGEPLDI LINGYLIAQG EVVVVADKYG VRITDIITPS ERMRRLSR UniProtKB: Flagellar motor switch protein FliN |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
---|---|
Buffer | pH: 8.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.5 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: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |