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- EMDB-26474: Cryo-EM of bundling pili from Pyrobaculum calidifontis -

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Basic information

Entry
Database: EMDB / ID: EMD-26474
TitleCryo-EM of bundling pili from Pyrobaculum calidifontis
Map dataCryo-EM and archaeal bundling filaments
Sample
  • Complex: extracellular bundling filaments
    • Protein or peptide: Pilin
Keywordshelical symmetry / biofilm / bundling pili / pili / PROTEIN FIBRIL
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPyrobaculum calidifontis (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWang F / Cvirkaite-Krupovic V / Krupovic M / Egelman EH
Funding support United States, 2 items
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, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26474.png

Downloads & links

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Map

FileDownload / File: emd_26474.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM and archaeal bundling filaments
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.194
Minimum - Maximum-0.38036638 - 0.8044624
Average (Standard dev.)0.00378532 (±0.023498746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_26474_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map b

Fileemd_26474_half_map_2.map
Annotationhalf map b
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : extracellular bundling filaments

EntireName: extracellular bundling filaments
Components
  • Complex: extracellular bundling filaments
    • Protein or peptide: Pilin

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Supramolecule #1: extracellular bundling filaments

SupramoleculeName: extracellular bundling filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pyrobaculum calidifontis (archaea)

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Macromolecule #1: Pilin

MacromoleculeName: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pyrobaculum calidifontis (archaea)
Molecular weightTheoretical: 22.16798 KDa
SequenceString: MARKKNYRPL IALAALAVAA LAMATLTFTN LTYWLINATL PPAMKYPGTD TTITRSDSSG YNRYVYVSYY YDPSTGYNVT RISIVGFTG DPTNYTNVLQ LCNKYYSGTL YAKLVAVGTV GTTNYESYIK DFRVYFVNPT TTPNYVQFQG TSVTQSATGS V SIGPGQCA ...String:
MARKKNYRPL IALAALAVAA LAMATLTFTN LTYWLINATL PPAMKYPGTD TTITRSDSSG YNRYVYVSYY YDPSTGYNVT RISIVGFTG DPTNYTNVLQ LCNKYYSGTL YAKLVAVGTV GTTNYESYIK DFRVYFVNPT TTPNYVQFQG TSVTQSATGS V SIGPGQCA TVGAYVLVDP SLPTSARDGK TVIATYQVNV VFSTSP

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 32.785 Å
Applied symmetry - Helical parameters - Δ&Phi: -77.404 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204565
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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