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- EMDB-60394: GerQ filaments from Bacillus amyloiquefaciens -

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Basic information

Entry
Database: EMDB / ID: EMD-60394
TitleGerQ filaments from Bacillus amyloiquefaciens
Map data
Sample
  • Cell: B. amyloiquefaciens
    • Protein or peptide: Spore coat protein GerQ
KeywordsEndospores / GerQ / spore coat protein / PROTEIN FIBRIL
Function / homologySpore coat protein GerQ / Spore coat protein (Spore_GerQ) / sporulation resulting in formation of a cellular spore / Spore coat protein GerQ
Function and homology information
Biological speciesBacillus amyloliquefaciens (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsKreutzberger M / Egelman E / Cao Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular architecture of the assembly of Bacillus spore coat protein GerQ revealed by cryo-EM.
Authors: Yijia Cheng / Mark A B Kreutzberger / Jianting Han / Edward H Egelman / Qin Cao /
Abstract: Protein filaments are ubiquitous in nature and have diverse biological functions. Cryo-electron microscopy (cryo-EM) enables the determination of atomic structures, even from native samples, and is ...Protein filaments are ubiquitous in nature and have diverse biological functions. Cryo-electron microscopy (cryo-EM) enables the determination of atomic structures, even from native samples, and is capable of identifying previously unknown filament species through high-resolution cryo-EM maps. In this study, we determine the structure of an unreported filament species from a cryo-EM dataset collected from Bacillus amyloiquefaciens biofilms. These filaments are composed of GerQ, a spore coat protein known to be involved in Bacillus spore germination. GerQ assembles into a structurally stable architecture consisting of rings containing nine subunits, which stacks to form filaments. Molecular dockings and model predictions suggest that this nine-subunit structure is suitable for binding CwlJ, a protein recruited by GerQ and essential for Ca-DPA induced spore germination. While the assembly state of GerQ within the spores and the direct interaction between GerQ and CwlJ have yet to be validated through further experiments, our findings provide valuable insights into the self-assembly of GerQ and enhance our understanding of its role in spore germination.
History
DepositionJun 4, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60394.png

Downloads & links

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Map

FileDownload / File: emd_60394.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.084
Minimum - Maximum-0.38838446 - 0.61936605
Average (Standard dev.)0.0013626055 (±0.028915398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60394_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_60394_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : B. amyloiquefaciens

EntireName: B. amyloiquefaciens
Components
  • Cell: B. amyloiquefaciens
    • Protein or peptide: Spore coat protein GerQ

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Supramolecule #1: B. amyloiquefaciens

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

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Macromolecule #1: Spore coat protein GerQ

MacromoleculeName: Spore coat protein GerQ / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Bacillus amyloliquefaciens (bacteria)
Molecular weightTheoretical: 20.359041 KDa
SequenceString:
MKPKKNQYQQ MQGMGMGMDM QGFQPQLGPN PYPQPQGQGS QMMPMQQQMT MPMQQGQQGF GGGFPGQPQQ QGGGSFQIPS GPSSSQNVP GMLPIEESYI ENILRLNRGK TATIYMTFEN SKEWNSKIFR GVIEAAGRDH IIISDPKTGT RYLLLTIYLD Y ITFDEEIA YTYPYSMSSY SPR

UniProtKB: Spore coat protein GerQ

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / 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: 34.2 Å
Applied symmetry - Helical parameters - Δ&Phi: -18.4 °
Applied symmetry - Helical parameters - Axial symmetry: C9 (9 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17798
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8zra:
GerQ filaments from Bacillus amyloiquefaciens

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