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- PDB-8zra: GerQ filaments from Bacillus amyloiquefaciens -

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Basic information

Entry
Database: PDB / ID: 8zra
TitleGerQ filaments from Bacillus amyloiquefaciens
ComponentsSpore coat protein GerQ
KeywordsPROTEIN FIBRIL / Endospores / GerQ / spore coat protein
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsKreutzberger, M. / Egelman, E. / Cao, Q.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spore coat protein GerQ
B: Spore coat protein GerQ
C: Spore coat protein GerQ
D: Spore coat protein GerQ
E: Spore coat protein GerQ
F: Spore coat protein GerQ
G: Spore coat protein GerQ
H: Spore coat protein GerQ
I: Spore coat protein GerQ
J: Spore coat protein GerQ
K: Spore coat protein GerQ
L: Spore coat protein GerQ
M: Spore coat protein GerQ
N: Spore coat protein GerQ
O: Spore coat protein GerQ
P: Spore coat protein GerQ
Q: Spore coat protein GerQ
R: Spore coat protein GerQ


Theoretical massNumber of molelcules
Total (without water)366,46318
Polymers366,46318
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Spore coat protein GerQ


Mass: 20359.041 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Bacillus amyloliquefaciens (bacteria) / References: UniProt: A0A9Q3LI79

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: B. amyloiquefaciens / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Bacillus amyloliquefaciens (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -18.4 ° / Axial rise/subunit: 34.2 Å / Axial symmetry: C9
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17798 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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