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- EMDB-71067: Structure of Natrinema sp. J7-2 Tafi pilus -

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Basic information

Entry
Database: EMDB / ID: EMD-71067
TitleStructure of Natrinema sp. J7-2 Tafi pilus
Map data
Sample
  • Complex: Tafi pilus
    • Protein or peptide: Pilin
KeywordsExtrcellular filament / Bundling pili / PROTEIN FIBRIL
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Uncharacterized protein
Function and homology information
Biological speciesNatrinema sp. J7-2 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSonani RR / Egelman EH
Funding support United States, 1 items
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: 2025
Title: Tat-dependent bundling pilus of a halophilic archaeon assembles by a strand donation mechanism and facilitates biofilm formation.
Authors: Ravi R Sonani / Ying Liu / Jialin Xiang / Virginija Cvirkaite-Krupovic / Shishen Du / Xiangdong Chen / Mart Krupovic / Edward H Egelman /
Abstract: Diverse extracellular filaments present on the surface of archaea mediate multiple key processes, such as motility, adhesion, and biofilm formation. Although several archaeal filament types have been ...Diverse extracellular filaments present on the surface of archaea mediate multiple key processes, such as motility, adhesion, and biofilm formation. Although several archaeal filament types have been characterized in considerable detail, many remain understudied, particularly those utilizing noncanonical secretion systems. Here, we describe the Tafi bundling pilus that facilitates biofilm formation in the haloarchaeon sp. J7-2. Unlike previously characterized archaeal pili, Tafi is secreted via the twin-arginine translocation (Tat) pathway, which transports fully folded proteins across the cytoplasmic membrane. Structural analysis reveals that although Tafi pili assemble via a canonical strand-donation mechanism, the pilin subunit (TafE) adopts a distinct structural topology that sets it apart from the previously characterized Sec-dependent pilins that form bundling pili in archaea. Sequence analyses show that TafE homologs are also present in thermophilic archaea from different phyla, but Tat-signal sequences are exclusive to pilins of halophilic archaea. Nevertheless, we find that Tat signal peptides in haloarchaeal TafE-like pili were exchanged back to the Sec signal peptides on multiple independent occasions. These findings expand our understanding of the diversity and evolution of archaeal extracellular filaments and highlight the Tat pathway as a route for pilus assembly in halophilic archaea.
History
DepositionJun 6, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71067.png

Downloads & links

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Map

FileDownload / File: emd_71067.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. 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: 0.99
Minimum - Maximum-0.08534011 - 12.639901999999999
Average (Standard dev.)-0.021322725 (±0.36550134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71067_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71067_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tafi pilus

EntireName: Tafi pilus
Components
  • Complex: Tafi pilus
    • Protein or peptide: Pilin

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Supramolecule #1: Tafi pilus

SupramoleculeName: Tafi pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Natrinema sp. J7-2 (archaea)

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Macromolecule #1: Pilin

MacromoleculeName: Pilin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Natrinema sp. J7-2 (archaea)
Molecular weightTheoretical: 21.695195 KDa
SequenceString: MKMNRRNVLV GLGTIVAGGG AALGTGAFSS VEADRTVSVA VAGDASSALA FDTSDSNGNQ YSDASSITNG TLELAFDSLG NSSGINLGA KTTFSPLFRT INNGSNNVNL SIYSSEGTIQ TSPTILDSYN AVIENTINDG NGNSLTIEYA FTDENDNSIV G DGTNGSSV ...String:
MKMNRRNVLV GLGTIVAGGG AALGTGAFSS VEADRTVSVA VAGDASSALA FDTSDSNGNQ YSDASSITNG TLELAFDSLG NSSGINLGA KTTFSPLFRT INNGSNNVNL SIYSSEGTIQ TSPTILDSYN AVIENTINDG NGNSLTIEYA FTDENDNSIV G DGTNGSSV SLDATGGSDP NEEVSLVIGV ADPGSSFDPS TTISGYLSEV TIVASSV

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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 33.36 Å
Applied symmetry - Helical parameters - Δ&Phi: -80.21 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Number images used: 36787
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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