6NAV | pdb_00006nav

Cryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

An extensively glycosylated archaeal pilus survives extreme conditions.

Wang, F.Cvirkaite-Krupovic, V.Kreutzberger, M.A.B.Su, Z.de Oliveira, G.A.P.Osinski, T.Sherman, N.DiMaio, F.Wall, J.S.Prangishvili, D.Krupovic, M.Egelman, E.H.

(2019) Nat Microbiol 4: 1401-1410

  • DOI: https://doi.org/10.1038/s41564-019-0458-x
  • Primary Citation Related Structures: 
    6NAV

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.

Macromolecule Content 

  • Total Structure Weight: 266.31 kDa 
  • Atom Count: 18,711 
  • Modeled Residue Count: 2,751 
  • Deposited Residue Count: 2,751 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
M9UD72
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U
131Saccharolobus islandicus LAL14/1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for M9UD72 (Saccharolobus islandicus LAL14/1)
Explore M9UD72 
Go to UniProtKB:  M9UD72
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM9UD72
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER
RECONSTRUCTIONRELION
MODEL REFINEMENTRosetta
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122510

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references