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- EMDB-36427: Flagellar fibrils from Bacillus amyloliquefaciens -

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Basic information

Entry
Database: EMDB / ID: EMD-36427
TitleFlagellar fibrils from Bacillus amyloliquefaciens
Map data
Sample
  • Cell: Bacillus amyloliquefaciens
    • Protein or peptide: Flagella
KeywordsFlagella / motor / fibril / PROTEIN FIBRIL
Biological speciesBacillus amyloliquefaciens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCao Q / Cheng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: Nat Commun / Year: 2023
Title: Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM.
Authors: Yijia Cheng / Jianting Han / Meinai Song / Shuqin Zhang / Qin Cao /
Abstract: Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab- ...Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils.
History
DepositionJun 5, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36427.png

Downloads & links

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Map

FileDownload / File: emd_36427.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å		1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-4.6935873 - 15.481427
Average (Standard dev.)-0.000000000001874 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36427_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36427_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Bacillus amyloliquefaciens

EntireName: Bacillus amyloliquefaciens (bacteria)
Components
  • Cell: Bacillus amyloliquefaciens
    • Protein or peptide: Flagella

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Supramolecule #1: Bacillus amyloliquefaciens

SupramoleculeName: Bacillus amyloliquefaciens / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus amyloliquefaciens (bacteria)

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Macromolecule #1: Flagella

MacromoleculeName: Flagella / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO
Source (natural)Organism: Bacillus amyloliquefaciens (bacteria)
Molecular weightTheoretical: 35.12884 KDa
SequenceString: MRINHNIAAL NTSRQLNAGS NAASKNMEKL SSGLRINRAG DDAAGLAISE KMRSQIRGLD MASKNAQDGI SLIQTSEGAL NETHSILQR MSELATQAAN DTNTDSDRSE LQKEMDQLAS EVTRISTDTE FNTKKLLDGT AQNLTFQIGA NEGQTMSLSI N KMDSESLK ...String:
MRINHNIAAL NTSRQLNAGS NAASKNMEKL SSGLRINRAG DDAAGLAISE KMRSQIRGLD MASKNAQDGI SLIQTSEGAL NETHSILQR MSELATQAAN DTNTDSDRSE LQKEMDQLAS EVTRISTDTE FNTKKLLDGT AQNLTFQIGA NEGQTMSLSI N KMDSESLK VGTTYTANDD GSKLVTADGK EATLVTDGSK GPNGYYDDAD KLVYQADSAL AKDTKVTKGI DISSSAKAAS SA LTTIKTA IDTVSSERAK LGAVQNRLEH TINNLGTSSE NLTSAESRIR DVDMASEMME YTKNNILTQA SQAMLAQANQ QPQ QVLQLL KG

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.6000000000000005 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.77 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153285
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5wjt

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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