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- EMDB-17579: Ex vivo L-ENA type pili from Bacillus paranthracis endospores -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-17579
TitleEx vivo L-ENA type pili from Bacillus paranthracis endospores
Map dataEx vivo L-ENA map
Sample
  • Organelle or cellular component: L-type endospore appendage
    • Protein or peptide: Ena3A
KeywordsEndospore / Pili / Protein / Fiber / Spore / Appendage / Bacillus paranthracis / PROTEIN FIBRIL
Function / homology:
Function and homology information
Biological speciesBacillus paranthracis (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 5.77 Å
AuthorsSleutel M / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
CitationJournal: To Be Published
Title: Bacillus paranthracis produces a novel class of ultra-stable endospore appendages that are decorated with collagen-like tip fibrillae
Authors: Sleutel M / Remaut H
History
DepositionJun 8, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17579.png

Downloads & links

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Map

FileDownload / File: emd_17579.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEx vivo L-ENA map
Voxel sizeX=Y=Z: 0.766 Å
Density
Contour LevelBy AUTHOR: 0.207
Minimum - Maximum-0.11069487 - 0.48682743
Average (Standard dev.)0.012180115 (±0.053039648)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 196.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17579_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ex vivo L-ENA half map A

Fileemd_17579_half_map_1.map
AnnotationEx vivo L-ENA half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ex vivo L-ENA half map B

Fileemd_17579_half_map_2.map
AnnotationEx vivo L-ENA half 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 : L-type endospore appendage

EntireName: L-type endospore appendage
Components
  • Organelle or cellular component: L-type endospore appendage
    • Protein or peptide: Ena3A

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Supramolecule #1: L-type endospore appendage

SupramoleculeName: L-type endospore appendage / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus paranthracis (bacteria) / Strain: NVH 0075-95 / Location in cell: spore surface
Molecular weightTheoretical: 18.03 kDa/nm

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Macromolecule #1: Ena3A

MacromoleculeName: Ena3A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus paranthracis (bacteria) / Strain: NVH 0075-95
SequenceString:
MAQIGNCCTE QLCCVNDAVC CTIILDDTGG TALPIWDDAT TFVINGTIMV ENNGTVGVGP TAALTVNGTA VGGFVVAPGE CRSITMNDIN SIAIVGAGTG TSSVKISFSI NYKF

UniProtKB: UNIPROTKB: PGS39_28750

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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 / Component - Formula: miliQ
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 8528 / Average electron dose: 62.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 43.82 Å
Applied symmetry - Helical parameters - Δ&Phi: 17.041 °
Applied symmetry - Helical parameters - Axial symmetry: C7 (7 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 5.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0.1) / Number images used: 8715
Startup modelType of model: INSILICO MODEL / In silico model: cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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