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- EMDB-48737: Cryo-EM structure of Natrinema sp. J7-2 Type IV pilus, PilA1 -

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Basic information

Entry
Database: EMDB / ID: EMD-48737
TitleCryo-EM structure of Natrinema sp. J7-2 Type IV pilus, PilA1
Map data
Sample
  • Complex: Type IV pilus
    • Protein or peptide: Archaeal Type IV pilin N-terminal domain-containing protein
KeywordsType IV pilus / Pilin / Biofilm / PROTEIN FIBRIL
Function / homology:
Function and homology information
Biological speciesNatrinema sp. J7-2 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 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: Cell Rep / Year: 2025
Title: A type IV pili-mediated mutualism between two co-resident temperate archaeal viruses and their host.
Authors: Jialin Xiang / Ravi R Sonani / Yangyang Wang / Zhao Chen / Weiyan Xiong / Jiangling Chen / Shuyu Li / Kang An / Yixuan Wang / Ying Liu / Mark A B Kreutzberger / Mart Krupovic / Edward H ...Authors: Jialin Xiang / Ravi R Sonani / Yangyang Wang / Zhao Chen / Weiyan Xiong / Jiangling Chen / Shuyu Li / Kang An / Yixuan Wang / Ying Liu / Mark A B Kreutzberger / Mart Krupovic / Edward H Egelman / Shishen Du / Xiangdong Chen /
Abstract: Co-resident temperate viruses are ubiquitous in prokaryotes, which interact with each other and affect their shared host. However, how such virus-virus and virus-host interactions play out in Archaea ...Co-resident temperate viruses are ubiquitous in prokaryotes, which interact with each other and affect their shared host. However, how such virus-virus and virus-host interactions play out in Archaea remains largely unexplored. Here, we discover a tripartite mutualistic interaction among the co-existing temperate viruses SNJ1 and SNJ2 and their host, haloarchaeon Natrinema sp. J7. We find that the SNJ2 provirus encodes two type IV pilins (T4Ps), which hijack the host secretion machinery to assemble into distinct filaments on the host cell surface. The SNJ2-encoded pili are dispensable for the SNJ2 infection but serve as receptors for SNJ1. As a quid pro quo, SNJ1 enhances the replication of SNJ2. Furthermore, the viral pili are the dominant filaments on the cell surface and promote biofilm formation and motility of the host. A number of SNJ2-like proviruses harbor T4P genes, suggesting that T4P-mediated virus-virus and virus-host interactions are widespread in Haloarchaea.
History
DepositionJan 21, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48737.png

Downloads & links

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Map

FileDownload / File: emd_48737.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.17096923 - 0.32604158
Average (Standard dev.)0.00071277574 (±0.019184127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpned mp

Fileemd_48737_additional_1.map
Annotationsharpned mp
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_48737_half_map_1.map
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Histogram

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Half map: #2

Fileemd_48737_half_map_2.map
Projections & Slices
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Sample components

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Entire : Type IV pilus

EntireName: Type IV pilus
Components
  • Complex: Type IV pilus
    • Protein or peptide: Archaeal Type IV pilin N-terminal domain-containing protein

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Supramolecule #1: Type IV pilus

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

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Macromolecule #1: Archaeal Type IV pilin N-terminal domain-containing protein

MacromoleculeName: Archaeal Type IV pilin N-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Natrinema sp. J7-2 (archaea)
Molecular weightTheoretical: 15.616163 KDa
Recombinant expressionOrganism: Natrinema sp. J7-2 (archaea)
SequenceString:
MDLKALKPKL VGSDNERAVS PVIGVILMVA ITVILAAVIA AFVLDLGGSV GQEAQAGVTI EVDESSQEIQ VEVTSMGNSD LVKLGGATD GIASNAGSTI SGDHTDMQTG DVVTMDGSSW SSTSGASASG TITAIAVIEE DETETQVASE EYDFS

UniProtKB: UNIPROTKB: I7CEX0

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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: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.95 Å
Applied symmetry - Helical parameters - Δ&Phi: 108.81 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35647
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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