+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21578 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM of the Pyrobaculum arsenaticum pilus | |||||||||
Map data | cryo-EM of the P. arsenaticum pilus | |||||||||
Sample |
| |||||||||
Function / homology | membrane => GO:0016020 / Uncharacterized protein Function and homology information | |||||||||
Biological species | Pyrobaculum arsenaticum (archaea) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Wang F / Baquero DP / Su Z / Beltran LC / Prangishvili D / Krupovic M / Egelman EH | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21578.map.gz | 70.1 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-21578-v30.xml emd-21578.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_21578.png | 111.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21578 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21578 | HTTPS FTP |
-Related structure data
Related structure data | 6w8uMC 6w8xC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_21578.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | cryo-EM of the P. arsenaticum pilus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Pyrobaculum arsenaticum pili
Entire | Name: Pyrobaculum arsenaticum pili |
---|---|
Components |
|
-Supramolecule #1: Pyrobaculum arsenaticum pili
Supramolecule | Name: Pyrobaculum arsenaticum pili / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Pyrobaculum arsenaticum (archaea) |
-Macromolecule #1: pilin
Macromolecule | Name: pilin / type: protein_or_peptide / ID: 1 / Number of copies: 41 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Pyrobaculum arsenaticum (archaea) |
Molecular weight | Theoretical: 14.49064 KDa |
Sequence | String: MTSLEIAIIV AIVLVIAIAV GWYLYTTFAA AGQQTGLTAT KATIYVTKDG NVYLNVTLVP QGAAQVAISS IEVAGVSIPC TSSNLVKAP GEYVIELSSV SVSVGQVLTG RIVLASGAIS PFTATVVAAD HVPSTENKLC SSQ |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6 |
---|---|
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 44.0 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: 5.26051 Å Applied symmetry - Helical parameters - Δ&Phi: 101.691 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Number images used: 210341 |
---|---|
CTF correction | Software - Name: Gctf |
Startup model | Type of model: OTHER Details: averaged cylinder using all segments, with random azimuthal angles |
Final angle assignment | Type: NOT APPLICABLE |