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Yorodumi- EMDB-25213: Cryo-EM structure of the enteropathogenic E. coli O127:H6 flagell... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25213 | |||||||||
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Title | Cryo-EM structure of the enteropathogenic E. coli O127:H6 flagellar filament | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Bacteria flagellar filament / motility / flagellar polymorphism / STRUCTURAL PROTEIN | |||||||||
Function / homology | : Function and homology information | |||||||||
Biological species | Escherichia coli O127:H6 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Kreutzberger MAB / Chatterjee S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments. Authors: Mark A B Kreutzberger / Richard C Sobe / Amber B Sauder / Sharanya Chatterjee / Alejandro Peña / Fengbin Wang / Jorge A Giron / Volker Kiessling / Tiago R D Costa / Vincent P Conticello / ...Authors: Mark A B Kreutzberger / Richard C Sobe / Amber B Sauder / Sharanya Chatterjee / Alejandro Peña / Fengbin Wang / Jorge A Giron / Volker Kiessling / Tiago R D Costa / Vincent P Conticello / Gad Frankel / Melissa M Kendall / Birgit E Scharf / Edward H Egelman / Abstract: Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in ...Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in many bacteria and their structures and functions are not conserved. Here, we show the atomic cryo-electron microscopy structures for flagellar filaments from enterohemorrhagic Escherichia coli O157:H7, enteropathogenic E. coli O127:H6, Achromobacter, and Sinorhizobium meliloti, where the outer domains dimerize or tetramerize to form either a sheath or a screw-like surface. These dimers are formed by 180° rotations of half of the outer domains. The outer domain sheath (ODS) plays a role in bacterial motility by stabilizing an intermediate waveform and prolonging the tumbling of E. coli cells. Bacteria with these ODS and screw-like flagellar filaments are commonly found in soil and human intestinal environments of relatively high viscosity suggesting a role for the dimerization in these environments. | |||||||||
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_25213.map.gz | 111.2 MB | EMDB map data format | |
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Header (meta data) | emd-25213-v30.xml emd-25213.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | emd_25213.png | 126.4 KB | ||
Filedesc metadata | emd-25213.cif.gz | 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25213 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25213 | HTTPS FTP |
-Validation report
Summary document | emd_25213_validation.pdf.gz | 619 KB | Display | EMDB validaton report |
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Full document | emd_25213_full_validation.pdf.gz | 618.6 KB | Display | |
Data in XML | emd_25213_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_25213_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25213 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25213 | HTTPS FTP |
-Related structure data
Related structure data | 7sn7MC 7sn4C 7sn9C 7sqdC 7sqjC 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_25213.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 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 : Bacterial flagellar filament
Entire | Name: Bacterial flagellar filament |
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Components |
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-Supramolecule #1: Bacterial flagellar filament
Supramolecule | Name: Bacterial flagellar filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli O127:H6 (bacteria) |
-Macromolecule #1: Flagellin
Macromolecule | Name: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli O127:H6 (bacteria) |
Molecular weight | Theoretical: 56.13973 KDa |
Sequence | String: QVINTNSLSL ITQNNINKNQ SALSSSIERL SSGLRINSAK DDAAGQAIAN RFTSNIKGLT QAARNANDGI SVAQTTEGAL SEINNNLQR IRELTVQAST GTNSDSDLDS IQDEIKSRLD EIDRVSGQTQ FNGVNVLAKD GSMKIQVGAN DGQTITIDLK K IDSDTLGL ...String: QVINTNSLSL ITQNNINKNQ SALSSSIERL SSGLRINSAK DDAAGQAIAN RFTSNIKGLT QAARNANDGI SVAQTTEGAL SEINNNLQR IRELTVQAST GTNSDSDLDS IQDEIKSRLD EIDRVSGQTQ FNGVNVLAKD GSMKIQVGAN DGQTITIDLK K IDSDTLGL NGFNVNGKGE TANTAATLKD MSGFTAAAAP GGTVGVTQYT DKSAVASSVD ILNAVAGADG NKVTTSADVG FG TPAAAVT YTYNKDTNSY SAASDDISSA NLAAFLNPQA RDTTKATVTI GGKDQDVNID KSGNLTAADD GAVLYMDATG NLT KNNAGG DTQATLAKVA TATGAKAATI QTDKGTFTSD GTAFDGASMS IDANTFANAV KNDTYTATVG AKTYSVTTGS AAAD TAYMS NGVLSDTPPT YYAQADGSIT TTEDAAAGKL VYKGSDGKLT TDTTSKAEST SDPLAALDDA ISQIDKFRSS LGAVQ NRLD SAVTNLNNTT TNLSEAQSRI QDADYATEVS NMSKAQIIQQ AGNSVLAKAN QVPQQVLSLL QG UniProtKB: UNIPROTKB: A0A2D0NRN6 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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 |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 269269 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |