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- PDB-6nav: Cryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus -

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Basic information

Entry
Database: PDB / ID: 6nav
TitleCryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus
ComponentsM9UD72
KeywordsSTRUCTURAL PROTEIN / helical symmetry / archaeal pilus
Function / homologyintegral component of membrane / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus islandicus LAL14/1 (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang, F. / Cvirkaite-Krupovic, V. / 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 Microbiol / Year: 2019
Title: An extensively glycosylated archaeal pilus survives extreme conditions.
Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Mark A B Kreutzberger / Zhangli Su / Guilherme A P de Oliveira / Tomasz Osinski / Nicholas Sherman / Frank DiMaio / Joseph S Wall / David ...Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Mark A B Kreutzberger / Zhangli Su / Guilherme A P de Oliveira / Tomasz Osinski / Nicholas Sherman / Frank DiMaio / Joseph S Wall / David Prangishvili / Mart Krupovic / Edward H Egelman /
Abstract: Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these ...Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these extracellular appendages to a very harsh environment. The pili, when removed from cells, resist digestion by trypsin or pepsin, and survive boiling in sodium dodecyl sulfate or 5 M guanidine hydrochloride. We used electron cryo-microscopy to determine the structure of these filaments at 4.1 Å resolution. An atomic model was built by combining the electron density map with bioinformatics without previous knowledge of the pilin sequence-an approach that should prove useful for assemblies where all of the components are not known. The atomic structure of the pilus was unusual, with almost one-third of the residues being either threonine or serine, and with many hydrophobic surface residues. While the map showed extra density consistent with glycosylation for only three residues, mass measurements suggested extensive glycosylation. We propose that this extensive glycosylation renders these filaments soluble and provides the remarkable structural stability. We also show that the overall fold of the archaeal pilin is remarkably similar to that of archaeal flagellin, establishing common evolutionary origins.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: M9UD72
B: M9UD72
C: M9UD72
D: M9UD72
E: M9UD72
F: M9UD72
G: M9UD72
H: M9UD72
I: M9UD72
J: M9UD72
K: M9UD72
L: M9UD72
M: M9UD72
N: M9UD72
O: M9UD72
P: M9UD72
Q: M9UD72
R: M9UD72
S: M9UD72
T: M9UD72
U: M9UD72


Theoretical massNumber of molelcules
Total (without water)266,30921
Polymers266,30921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
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TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
M9UD72


Mass: 12681.375 Da / Num. of mol.: 21 / Source method: isolated from a natural source
Source: (natural) Sulfolobus islandicus LAL14/1 (acidophilic)
References: UniProt: M9UD72

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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: Sulfolobus islandicus LAL14/1 Pilus / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sulfolobus islandicus LAL14/1 (acidophilic)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELDBright-field microscopy
Image recordingAverage exposure time: 2 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Details: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2.

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Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
IDNameCategory
1EMAN2particle selection
2EPUimage acquisition
4GctfCTF correction
12SPIDER3D reconstruction
13RELION3D reconstruction
14Rosettamodel refinement
15PHENIXmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 104.97 ° / Axial rise/subunit: 4.94 Å / Axial symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: OTHER / Num. of particles: 181070 / Details: MODEL:MAP FSC, D99 / Symmetry type: HELICAL

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