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- PDB-7ueg: Cryo-EM of bundling pili from Pyrobaculum calidifontis -

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Basic information

Entry
Database: PDB / ID: 7ueg
TitleCryo-EM of bundling pili from Pyrobaculum calidifontis
ComponentsPilin
KeywordsPROTEIN FIBRIL / helical symmetry / biofilm / bundling pili / pili
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPyrobaculum calidifontis (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsWang, F. / Cvirkaite-Krupovic, V. / Krupovic, M. / Egelman, E.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Archaeal bundling pili of reveal similarities between archaeal and bacterial biofilms.
Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Mart Krupovic / Edward H Egelman /
Abstract: While biofilms formed by bacteria have received great attention due to their importance in pathogenesis, much less research has been focused on the biofilms formed by archaea. It has been known that ...While biofilms formed by bacteria have received great attention due to their importance in pathogenesis, much less research has been focused on the biofilms formed by archaea. It has been known that extracellular filaments in archaea, such as type IV pili, hami, and cannulae, play a part in the formation of archaeal biofilms. We have used cryo-electron microscopy to determine the atomic structure of a previously uncharacterized class of archaeal surface filaments from hyperthermophilic These filaments, which we call archaeal bundling pili (ABP), assemble into highly ordered bipolar bundles. The bipolar nature of these bundles most likely arises from the association of filaments from at least two different cells. The component protein, AbpA, shows homology, both at the sequence and structural level, to the bacterial protein TasA, a major component of the extracellular matrix in bacterial biofilms, contributing to biofilm stability. We show that AbpA forms very stable filaments in a manner similar to the donor-strand exchange of bacterial TasA fibers and chaperone-usher pathway pili where a β-strand from one subunit is incorporated into a β-sheet of the next subunit. Our results reveal likely mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms, and suggest that there could be many other archaeal surface filaments that are as yet uncharacterized.
History
DepositionMar 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilin
E: Pilin
B: Pilin
C: Pilin
D: Pilin
F: Pilin


Theoretical massNumber of molelcules
Total (without water)133,0086
Polymers133,0086
Non-polymers00
Water00
1
A: Pilin
E: Pilin
B: Pilin
C: Pilin
D: Pilin
F: Pilin
x 6


Theoretical massNumber of molelcules
Total (without water)798,04736
Polymers798,04736
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation5
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 6 / Rise per n subunits: 32.785 Å / Rotation per n subunits: -77.404 °)

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Components

#1: Protein
Pilin


Mass: 22167.980 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum calidifontis (archaea) / References: UniProt: A3MUL8

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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: extracellular bundling filaments / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pyrobaculum calidifontis (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: FEI TITAN 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: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -77.404 ° / Axial rise/subunit: 32.785 Å / Axial symmetry: C1
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204565 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02859850
ELECTRON MICROSCOPYf_angle_d0.73182362
ELECTRON MICROSCOPYf_dihedral_angle_d5.5878526
ELECTRON MICROSCOPYf_chiral_restr0.0499744
ELECTRON MICROSCOPYf_plane_restr0.00610332

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