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Yorodumi- EMDB-10362: Cryo-EM structure of the wild-type flagellar filament of the Firm... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10362 | |||||||||||||||
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Title | Cryo-EM structure of the wild-type flagellar filament of the Firmicute Kurthia | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Gram-Positive Bacteria Flagella / Helical / Wild-Type / protein fibril | |||||||||||||||
Function / homology | bacterial-type flagellum filament / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / Flagellin Function and homology information | |||||||||||||||
Biological species | Kurthia sp. 11kri321 (bacteria) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Blum TB / Abrahams JP | |||||||||||||||
Funding support | Switzerland, 4 items
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Citation | Journal: Sci Rep / Year: 2019 Title: The wild-type flagellar filament of the Firmicute Kurthia at 2.8 Å resolution in vivo. Authors: Thorsten B Blum / Sevasti Filippidou / Mathilda Fatton / Pilar Junier / Jan Pieter Abrahams / Abstract: Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the ...Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the filament's supercoil. So far, all studied functional filaments are composed of a mixture of L- and R-state flagellin monomers. Here we show in a study of the wild type Firmicute Kurthia sp., that curved, functional filaments can adopt a conformation in vivo that is closely related to a uniform, all-L-state. This sheds additional light on transitions of the flagellar supercoil and uniquely reveals the atomic structure of a wild-type flagellar filament in vivo, including six residues showing clearly densities of O-linked glycosylation. | |||||||||||||||
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_10362.map.gz | 57.4 MB | EMDB map data format | |
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Header (meta data) | emd-10362-v30.xml emd-10362.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10362_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_10362.png | 65.8 KB | ||
Filedesc metadata | emd-10362.cif.gz | 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10362 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10362 | HTTPS FTP |
-Validation report
Summary document | emd_10362_validation.pdf.gz | 650.1 KB | Display | EMDB validaton report |
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Full document | emd_10362_full_validation.pdf.gz | 649.7 KB | Display | |
Data in XML | emd_10362_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_10362_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10362 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10362 | HTTPS FTP |
-Related structure data
Related structure data | 6t17MC 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_10362.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Flagellar Filament
Entire | Name: Flagellar Filament |
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Components |
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-Supramolecule #1: Flagellar Filament
Supramolecule | Name: Flagellar Filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Kurthia sp. 11kri321 (bacteria) |
-Macromolecule #1: Flagellin
Macromolecule | Name: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 44 / Enantiomer: LEVO |
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Source (natural) | Organism: Kurthia sp. 11kri321 (bacteria) |
Molecular weight | Theoretical: 29.530055 KDa |
Recombinant expression | Organism: Kurthia sp. 11kri321 (bacteria) |
Sequence | String: MRIQHNIAAL NTHRNLAANN AAASKNLEKL SSGFKINRAG DDAAGLAISE KMRGQISGLN MASKNSSDAI SLIQTAEGGL NETHAILQR MRELAVQSRN DTNDEATNDR SNLNDELKQL QEEITRISSQ MEFNNKKLLD GSQSTNGLTF QIGANAGQTI T MKISTMSA ...String: MRIQHNIAAL NTHRNLAANN AAASKNLEKL SSGFKINRAG DDAAGLAISE KMRGQISGLN MASKNSSDAI SLIQTAEGGL NETHAILQR MRELAVQSRN DTNDEATNDR SNLNDELKQL QEEITRISSQ MEFNNKKLLD GSQSTNGLTF QIGANAGQTI T MKISTMSA TKLGVDAAKA SISKGTAASK AIKSIDDAIN TVSKTRSALG AVQNRLEHTI NNLGTSAENL TAAESRIRDT DM AAEMMAF TKNNILTQAA QSMLAQANQQ PQGVLQLLQ UniProtKB: Flagellin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.3 |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 86.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |