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- EMDB-11592: 3D cryoEM map of ex vivo Ena1 from Bacillus cereus -

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Basic information

Entry
Database: EMDB / ID: EMD-11592
Title3D cryoEM map of ex vivo Ena1 from Bacillus cereus
Map data
Sample
  • Organelle or cellular component: Ex vivo S-type Ena
Function / homologyEndospore appendages core / Endospore appendages / DUF3992 domain-containing protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsPradhan B / Sleutel M / Liedtke J / Lindback T / Llarena AK / Brynildsrud O / Aspholm M / Remaut H
Funding support Belgium, 1 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Citation
Journal: EMBO J / Year: 2021
Title: Endospore Appendages: a novel pilus superfamily from the endospores of pathogenic Bacilli.
Authors: Brajabandhu Pradhan / Janine Liedtke / Mike Sleutel / Toril Lindbäck / Ephrem Debebe Zegeye / Kristin O Sullivan / Ann-Katrin Llarena / Ola Brynildsrud / Marina Aspholm / Han Remaut /
Abstract: Bacillus cereus sensu lato is a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity ...Bacillus cereus sensu lato is a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity and function. Here, we isolate endospore appendages (Enas) from the food poisoning outbreak strain B. cereus NVH 0075-95 and find proteinaceous fibers of two main morphologies: S- and L-Ena. By using cryoEM and 3D helical reconstruction of S-Enas, we show these to represent a novel class of Gram-positive pili. S-Enas consist of single domain subunits with jellyroll topology that are laterally stacked by β-sheet augmentation. S-Enas are longitudinally stabilized by disulfide bonding through N-terminal connector peptides that bridge the helical turns. Together, this results in flexible pili that are highly resistant to heat, drought, and chemical damage. Phylogenomic analysis reveals a ubiquitous presence of the ena-gene cluster in the B. cereus group, which include species of clinical, environmental, and food importance. We propose Enas to represent a new class of pili specifically adapted to the harsh conditions encountered by bacterial spores.
#1: Journal: Biorxiv / Year: 2020
Title: Bacillus endospore appendages form a novel family of disulfide-linked pili
Authors: Pradhan B / Liedtke J / Sleutel M / Lindback T / Llarena AK / Brynildsrud O / Aspholm M / Remaut H
History
DepositionAug 6, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11592.png

Downloads & links

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Map

FileDownload / File: emd_11592.map.gz / Format: CCP4 / Size: 15.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 157 pix.
= 128.74 Å		0.82 Å/pix.
x 157 pix.
= 128.74 Å		0.82 Å/pix.
x 169 pix.
= 138.58 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.02 / Movie #1: 1.02
Minimum - Maximum-5.392833 - 8.832743
Average (Standard dev.)-1.1151092e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin726572
Dimensions157169157
Spacing157157169
CellA: 128.74 Å / B: 128.74 Å / C: 138.58 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z157157169
origin x/y/z0.0000.0000.000
length x/y/z128.740128.740138.580
α/β/γ90.00090.00090.000
start NX/NY/NZ727265
NX/NY/NZ157157169
MAP C/R/S321
start NC/NR/NS657272
NC/NR/NS169157157
D min/max/mean-5.3938.833-0.000

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Supplemental data

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Sample components

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Entire : Ex vivo S-type Ena

EntireName: Ex vivo S-type Ena
Components
  • Organelle or cellular component: Ex vivo S-type Ena

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Supramolecule #1: Ex vivo S-type Ena

SupramoleculeName: Ex vivo S-type Ena / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Bacillus cereus (bacteria) / Strain: NVH 0075-95

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
GridModel: Quantifoil / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 2000 / Average electron dose: 62.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 60000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 3.22937 Å
Applied symmetry - Helical parameters - Δ&Phi: 31.0338 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 42822
CTF correctionSoftware - Name: CTFFIND (ver. 4.2)
Segment selectionNumber selected: 53501 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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