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

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Open data


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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: To Be Published
Title: Structure of Natrinema sp. J7-2 Tafi pilus
Authors: Sonani RR / Egelman EH
History
DepositionJun 6, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 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
Brightness
Contrast
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

Projections

Slices (1/2)
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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