+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21579 | |||||||||
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Title | Cryo-EM of the S. solfataricus pilus | |||||||||
Map data | cryo-EM of the S. solfataricus pilus | |||||||||
Sample |
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Keywords | helical symmetry / archaeal pilus / Type IV pilus / PROTEIN FIBRIL | |||||||||
Function / homology | membrane => GO:0016020 / Uncharacterized protein Function and homology information | |||||||||
Biological species | Saccharolobus solfataricus (archaea) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Wang F / Baquero DP | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: The structures of two archaeal type IV pili illuminate evolutionary relationships. Authors: Fengbin Wang / Diana P Baquero / Zhangli Su / Leticia C Beltran / David Prangishvili / Mart Krupovic / Edward H Egelman / Abstract: We have determined the cryo-electron microscopic (cryo-EM) structures of two archaeal type IV pili (T4P), from Pyrobaculum arsenaticum and Saccharolobus solfataricus, at 3.8 Å and 3.4 Å ...We have determined the cryo-electron microscopic (cryo-EM) structures of two archaeal type IV pili (T4P), from Pyrobaculum arsenaticum and Saccharolobus solfataricus, at 3.8 Å and 3.4 Å resolution, respectively. This triples the number of high resolution archaeal T4P structures, and allows us to pinpoint the evolutionary divergence of bacterial T4P, archaeal T4P and archaeal flagellar filaments. We suggest that extensive glycosylation previously observed in T4P of Sulfolobus islandicus is a response to an acidic environment, as at even higher temperatures in a neutral environment much less glycosylation is present for Pyrobaculum than for Sulfolobus and Saccharolobus pili. Consequently, the Pyrobaculum filaments do not display the remarkable stability of the Sulfolobus filaments in vitro. We identify the Saccharolobus and Pyrobaculum T4P as host receptors recognized by rudivirus SSRV1 and tristromavirus PFV2, respectively. Our results illuminate the evolutionary relationships among bacterial and archaeal T4P filaments and provide insights into archaeal virus-host interactions. | |||||||||
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_21579.map.gz | 68.2 MB | EMDB map data format | |
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Header (meta data) | emd-21579-v30.xml emd-21579.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | emd_21579.png | 156.3 KB | ||
Filedesc metadata | emd-21579.cif.gz | 4.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21579 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21579 | HTTPS FTP |
-Validation report
Summary document | emd_21579_validation.pdf.gz | 528.5 KB | Display | EMDB validaton report |
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Full document | emd_21579_full_validation.pdf.gz | 528 KB | Display | |
Data in XML | emd_21579_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_21579_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21579 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21579 | HTTPS FTP |
-Related structure data
Related structure data | 6w8xMC 6w8uC 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_21579.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM of the S. solfataricus pilus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Sulfolobus solfataricus pilus
Entire | Name: Sulfolobus solfataricus pilus |
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Components |
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-Supramolecule #1: Sulfolobus solfataricus pilus
Supramolecule | Name: Sulfolobus solfataricus pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharolobus solfataricus (archaea) |
-Macromolecule #1: pilin
Macromolecule | Name: pilin / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharolobus solfataricus (archaea) |
Molecular weight | Theoretical: 12.854739 KDa |
Sequence | String: LSGAVTALIL VIASVIIALV VVGFAFGLFG AFTGQGTVAQ VGTATLSAST LTLTVTLKNT GASTQVTGVL INGNSGSVSG MTTISAGVN TYTITISIGS ISTTLRGLVG STISLTLILS NGETVTVSAI VTS UniProtKB: Uncharacterized protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN 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
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.97404 Å Applied symmetry - Helical parameters - Δ&Phi: 104.573 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Number images used: 579710 |
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Startup model | Type of model: OTHER Details: averaged cylinder using all segments, with random azimuthal angles |
Final angle assignment | Type: NOT APPLICABLE |