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- PDB-8fjs: Structure of the Saccharolobus solfataricus archaeal type IV pilu... -

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Basic information

Entry
Database: PDB / ID: 8fjs
TitleStructure of the Saccharolobus solfataricus archaeal type IV pilus at 3 Angstrom resolution
ComponentsPilin_N domain-containing protein
KeywordsSTRUCTURAL PROTEIN / Archaea / type IV pili
Function / homologymembrane / DUF973 family protein
Function and homology information
Biological speciesSaccharolobus solfataricus (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å
AuthorsKreutzberger, M.A. / Wang, F. / Krupovic, M. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: The evolution of archaeal flagellar filaments.
Authors: Mark A B Kreutzberger / Virginija Cvirkaite-Krupovic / Ying Liu / Diana P Baquero / Junfeng Liu / Ravi R Sonani / Chris R Calladine / Fengbin Wang / Mart Krupovic / Edward H Egelman /
Abstract: Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single ...Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
History
DepositionDec 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pilin_N domain-containing protein
B: Pilin_N domain-containing protein
C: Pilin_N domain-containing protein
D: Pilin_N domain-containing protein
E: Pilin_N domain-containing protein
F: Pilin_N domain-containing protein
G: Pilin_N domain-containing protein
H: Pilin_N domain-containing protein
I: Pilin_N domain-containing protein
J: Pilin_N domain-containing protein
K: Pilin_N domain-containing protein
L: Pilin_N domain-containing protein
M: Pilin_N domain-containing protein
N: Pilin_N domain-containing protein
O: Pilin_N domain-containing protein
P: Pilin_N domain-containing protein
Q: Pilin_N domain-containing protein
R: Pilin_N domain-containing protein
S: Pilin_N domain-containing protein
T: Pilin_N domain-containing protein
U: Pilin_N domain-containing protein
V: Pilin_N domain-containing protein
W: Pilin_N domain-containing protein
X: Pilin_N domain-containing protein
Y: Pilin_N domain-containing protein


Theoretical massNumber of molelcules
Total (without water)355,83425
Polymers355,83425
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Pilin_N domain-containing protein


Mass: 14233.371 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A7S9IHX8

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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: Archaeal type IV pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19rc4_4035: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 104.572 ° / Axial rise/subunit: 4.976 Å / Axial symmetry: C1
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 725012 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222650
ELECTRON MICROSCOPYf_angle_d0.42631050
ELECTRON MICROSCOPYf_dihedral_angle_d3.2143350
ELECTRON MICROSCOPYf_chiral_restr0.0444600
ELECTRON MICROSCOPYf_plane_restr0.0013675

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