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Yorodumi- EMDB-27026: Cryo-EM structure of the supercoiled S. islandicus REY15A archaea... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27026 | |||||||||
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Title | Cryo-EM structure of the supercoiled S. islandicus REY15A archaeal flagellar filament | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Archaea / Motility / supercoiling / STRUCTURAL PROTEIN | |||||||||
Function / homology | archaeal-type flagellum / Flagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / membrane / Flagellin Function and homology information | |||||||||
Biological species | Sulfolobus islandicus (acidophilic) / Sulfolobus islandicus REY15A (acidophilic) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Kreutzberger MAB / Liu J / Krupovic M / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell / Year: 2022 Title: Convergent evolution in the supercoiling of prokaryotic flagellar filaments. Authors: Mark A B Kreutzberger / Ravi R Sonani / Junfeng Liu / Sharanya Chatterjee / Fengbin Wang / Amanda L Sebastian / Priyanka Biswas / Cheryl Ewing / Weili Zheng / Frédéric Poly / Gad Frankel / ...Authors: Mark A B Kreutzberger / Ravi R Sonani / Junfeng Liu / Sharanya Chatterjee / Fengbin Wang / Amanda L Sebastian / Priyanka Biswas / Cheryl Ewing / Weili Zheng / Frédéric Poly / Gad Frankel / B F Luisi / Chris R Calladine / Mart Krupovic / Birgit E Scharf / Edward H Egelman / Abstract: The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of ...The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of bacterial type IV pili. How these prokaryotic flagellar filaments, each composed of thousands of copies of identical subunits, can form stable supercoils under torsional stress is a fascinating puzzle for which structural insights have been elusive. Advances in cryoelectron microscopy (cryo-EM) make it now possible to directly visualize the basis for supercoiling, and here, we show the atomic structures of supercoiled bacterial and archaeal flagellar filaments. For the bacterial flagellar filament, we identify 11 distinct protofilament conformations with three broad classes of inter-protomer interface. For the archaeal flagellar filament, 10 protofilaments form a supercoil geometry supported by 10 distinct conformations, with one inter-protomer discontinuity creating a seam inside of the curve. Our results suggest that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27026.map.gz | 34.8 MB | EMDB map data format | |
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Header (meta data) | emd-27026-v30.xml emd-27026.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_27026.png | 44.3 KB | ||
Masks | emd_27026_msk_1.map | 926.9 MB | Mask map | |
Filedesc metadata | emd-27026.cif.gz | 5 KB | ||
Others | emd_27026_half_map_1.map.gz emd_27026_half_map_2.map.gz | 858.6 MB 858.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27026 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27026 | HTTPS FTP |
-Validation report
Summary document | emd_27026_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_27026_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_27026_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | emd_27026_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27026 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27026 | HTTPS FTP |
-Related structure data
Related structure data | 8cwmMC 8cviC 8cxmC 8cyeC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27026.map.gz / Format: CCP4 / Size: 926.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27026_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27026_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27026_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Archaeal flagellar filament
Entire | Name: Archaeal flagellar filament |
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Components |
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-Supramolecule #1: Archaeal flagellar filament
Supramolecule | Name: Archaeal flagellar filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Sulfolobus islandicus (acidophilic) / Strain: REY15A |
-Macromolecule #1: Flagellin
Macromolecule | Name: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: Sulfolobus islandicus REY15A (acidophilic) / Strain: REY15A |
Molecular weight | Theoretical: 33.1335 KDa |
Sequence | String: MNTKKMLKEY NKKVKRKGLA GLDTAIILIA FIITASVLAY VAINMGLFVT QKAKSTINKG EETASTALTL SGSVLYAVNY PSNTRSYWI YFTVSPSSGV SSVELSPSTT AISFTASAEG ISYSNIYEYT LLTVSPSELA NQVYANGQYL DLVNQQTNAG Q TYVYYPNP ...String: MNTKKMLKEY NKKVKRKGLA GLDTAIILIA FIITASVLAY VAINMGLFVT QKAKSTINKG EETASTALTL SGSVLYAVNY PSNTRSYWI YFTVSPSSGV SSVELSPSTT AISFTASAEG ISYSNIYEYT LLTVSPSELA NQVYANGQYL DLVNQQTNAG Q TYVYYPNP YYALLALNYT LSKIDKVSPS PLYITTTTPS SATQIYPFLA HDNMFTFTLN ISGTLVTYYA FVNQTFAFTY PV AGDPLIG SAIAPAGSVI GVMILFGPDL GSHVFQYQTI TIQITPNIGS PLTISEYVYQ PEGSVSVIG UniProtKB: Flagellin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 3 |
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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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.33 CUT-OFF / Number images used: 51914 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |