+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13546 | |||||||||
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Title | Sulfolobus acidocaldarius 0406 filament. | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Isupov MN / Gaines M / Daum B | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Electron cryo-microscopy reveals the structure of the archaeal thread filament. Authors: Matthew C Gaines / Michail N Isupov / Shamphavi Sivabalasarma / Risat Ul Haque / Mathew McLaren / Clara L Mollat / Patrick Tripp / Alexander Neuhaus / Vicki A M Gold / Sonja-Verena Albers / Bertram Daum / Abstract: Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal ...Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13546.map.gz | 181.6 MB | EMDB map data format | |
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Header (meta data) | emd-13546-v30.xml emd-13546.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_13546.png | 43.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13546 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13546 | HTTPS FTP |
-Validation report
Summary document | emd_13546_validation.pdf.gz | 311.3 KB | Display | EMDB validaton report |
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Full document | emd_13546_full_validation.pdf.gz | 310.9 KB | Display | |
Data in XML | emd_13546_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_13546_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13546 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13546 | HTTPS FTP |
-Related structure data
Related structure data | 7pnbMC 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_13546.map.gz / Format: CCP4 / Size: 216 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: 1.047 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Filament
Entire | Name: Filament |
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Components |
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-Supramolecule #1: Filament
Supramolecule | Name: Filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Sulfolobus acidocaldarius (acidophilic) |
-Macromolecule #1: Sulfolobus acidocaldarius 0406 filament.
Macromolecule | Name: Sulfolobus acidocaldarius 0406 filament. / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO |
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Source (natural) | Organism: Sulfolobus acidocaldarius (acidophilic) |
Molecular weight | Theoretical: 22.291539 KDa |
Recombinant expression | Organism: Sulfolobus acidocaldarius (acidophilic) |
Sequence | String: MNKKRLLLLS VFLVSVFVPV LVADVIYYYQ GQITVGNVAP PMYFAIQPNG NAKIGNNSNV PSYINAQPSS GGSGFTAQVN ITNATYNYY FNFMGLAVSK TGYIYLAKVA YSYTATNNPI QNATLYIMNQ QGQIVYKYKL IVNGVVNSTL PSTPLQINSG S YIVSLLIV ...String: MNKKRLLLLS VFLVSVFVPV LVADVIYYYQ GQITVGNVAP PMYFAIQPNG NAKIGNNSNV PSYINAQPSS GGSGFTAQVN ITNATYNYY FNFMGLAVSK TGYIYLAKVA YSYTATNNPI QNATLYIMNQ QGQIVYKYKL IVNGVVNSTL PSTPLQINSG S YIVSLLIV PYQGTLPKTP SNDLATITVN FGFSPMTASP PPIPLPSP |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 3 |
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Vitrification | Cryogen name: ETHANE |
Details | Mixed population of filaments isolated from Sulfolobus acidocaldarius |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 6272 / Average electron dose: 42.33 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
Final reconstruction | Number classes used: 1 Applied symmetry - Helical parameters - Δz: 31.649 Å Applied symmetry - Helical parameters - Δ&Phi: -103.234 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 188620 |
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Segment selection | Number selected: 410270 / Software - Name: cryoSPARC (ver. 3.2.0) Software - details: cryoSPARC filament tracer was used to automatically pick particles |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.2.0) |
-Atomic model buiding 1
Details | Jligand was used for preparing dictionaries for an unusual sugars and an isopeptide link beween main chain nitrogen of the N-terminal D25 and C gamma of N57 from N-2 monomer in the filament. |
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Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
Output model | PDB-7pnb: |