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- PDB-6w8u: Cryo-EM of the Pyrobaculum arsenaticum pilus -

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Basic information

Entry
Database: PDB / ID: 6w8u
TitleCryo-EM of the Pyrobaculum arsenaticum pilus
Componentspilin
KeywordsPROTEIN FIBRIL / helical symmetry / archaeal pilus / Type IV pilus
Function / homologymembrane => GO:0016020 / Uncharacterized protein
Function and homology information
Biological speciesPyrobaculum arsenaticum (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWang, F. / Baquero, D.P. / Su, Z. / Beltran, L.C. / Prangishvili, D. / Krupovic, M. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: 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
DepositionMar 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: pilin
B: pilin
C: pilin
D: pilin
E: pilin
F: pilin
G: pilin
H: pilin
I: pilin
J: pilin
K: pilin
L: pilin
M: pilin
N: pilin
O: pilin
P: pilin
Q: pilin
R: pilin
S: pilin
T: pilin
U: pilin
V: pilin
W: pilin
X: pilin
Y: pilin
Z: pilin
a: pilin
b: pilin
c: pilin
d: pilin
e: pilin
f: pilin
g: pilin
h: pilin
i: pilin
j: pilin
k: pilin
l: pilin
m: pilin
n: pilin
o: pilin


Theoretical massNumber of molelcules
Total (without water)594,11641
Polymers594,11641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area192430 Å2
ΔGint-1677 kcal/mol
Surface area165630 Å2
SymmetryHelical 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 °)

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Components

#1: Protein ...
pilin


Mass: 14490.640 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum arsenaticum (archaea) / References: UniProt: A4WH64

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Pyrobaculum arsenaticum pili / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pyrobaculum arsenaticum (archaea)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 2 sec. / Electron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1EMAN2particle selection
2Latitudeimage acquisition
4GctfCTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 101.691 ° / Axial rise/subunit: 5.26051 Å / Axial symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 210341 / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Symmetry type: HELICAL

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