+Open data
-Basic information
Entry | Database: PDB / ID: 6w8u | ||||||
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Title | Cryo-EM of the Pyrobaculum arsenaticum pilus | ||||||
Components | pilin | ||||||
Keywords | PROTEIN FIBRIL / helical symmetry / archaeal pilus / Type IV pilus | ||||||
Function / homology | membrane / Class III signal peptide-containing protein Function and homology information | ||||||
Biological species | Pyrobaculum arsenaticum (archaea) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Authors | Wang, F. / Baquero, D.P. / Su, Z. / Beltran, L.C. / Prangishvili, D. / Krupovic, M. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6w8u.cif.gz | 864.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w8u.ent.gz | 738.7 KB | Display | PDB format |
PDBx/mmJSON format | 6w8u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w8u_validation.pdf.gz | 771.4 KB | Display | wwPDB validaton report |
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Full document | 6w8u_full_validation.pdf.gz | 773.9 KB | Display | |
Data in XML | 6w8u_validation.xml.gz | 108.7 KB | Display | |
Data in CIF | 6w8u_validation.cif.gz | 183.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/6w8u ftp://data.pdbj.org/pub/pdb/validation_reports/w8/6w8u | HTTPS FTP |
-Related structure data
Related structure data | 21578MC 6w8xC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 41 / Rise per n subunits: 5.26051 Å / Rotation per n subunits: 101.691 °) |
-Components
#1: Protein | Mass: 14490.640 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum arsenaticum (archaea) / References: UniProt: A4WH64 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Pyrobaculum arsenaticum pili / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Pyrobaculum arsenaticum (archaea) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Humidity: 90 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 2 sec. / Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Helical symmerty | Angular rotation/subunit: 101.691 ° / Axial rise/subunit: 5.26051 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 210341 / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Symmetry type: HELICAL |