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- EMDB-62902: Bacillus subtilis endospore crust protein CgeA -

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Basic information

Entry
Database: EMDB / ID: EMD-62902
TitleBacillus subtilis endospore crust protein CgeA
Map data
Sample
  • Complex: Hexameric complex of Bacillus subtilis endospore crust protein CgeA
    • Protein or peptide: Spore crust protein CgeA
KeywordsGlycoprotein / Sporulation / Bacillus subtilis / STRUCTURAL PROTEIN
Function / homologySpore crust protein CgeA
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsPark M / Kim D / Baek Y / Hyun J / Ha NC
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Microbiol / Year: 2025
Title: Cryo-EM structure of the glycosylated protein CgeA in the crust of Bacillus subtilis endospores.
Authors: Migak Park / Doyeon Kim / Yeongjin Baek / Eunbyul Jo / Jaekyung Hyun / Nam-Chul Ha /
Abstract: The Bacillus subtilis spore crust is an exceptionally robust proteinaceous layer that protects spores under extreme environmental conditions. Among its key components, CgeA, a glycosylation- ...The Bacillus subtilis spore crust is an exceptionally robust proteinaceous layer that protects spores under extreme environmental conditions. Among its key components, CgeA, a glycosylation-associated protein, plays a critical role in modifying crust properties through its glycosylated moiety, enhancing spore dispersal in aqueous environments. In this study, we present the high-resolution cryo-electron microscopy structure of the core region of CgeA at 3.05 Å resolution, revealing a doughnut-like hexameric assembly. The N-terminal regions are disordered, whereas the C-terminal region forms the core of the hexamer. Although the loop containing Thr112 was not resolved in the density map, its location can be inferred from surrounding residues, suggesting that Thr112 is situated on the exposed surface of the hexamer. On the opposite face, a distinct electrostatic pattern is observed, featuring a negatively charged central pore and a positively charged outer surface. Modeling and biochemical studies with the putative glycosyltransferase CgeB provide insights into how the glycosyl group is transferred to Thr112. This study offers a molecular-level understanding of the assembly, glycosylation, and environmental adaptability of the B. subtilis spore crust, with valuable implications for controlling spore formation in industrial applications.
History
DepositionDec 30, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62902.png

Downloads & links

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Map

FileDownload / File: emd_62902.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 192 pix.
= 158.976 Å		0.83 Å/pix.
x 192 pix.
= 158.976 Å		0.83 Å/pix.
x 192 pix.
= 158.976 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.20553471 - 0.32617107
Average (Standard dev.)-0.00005356577 (±0.0126782395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 158.976 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62902_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62902_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric complex of Bacillus subtilis endospore crust protein CgeA

EntireName: Hexameric complex of Bacillus subtilis endospore crust protein CgeA
Components
  • Complex: Hexameric complex of Bacillus subtilis endospore crust protein CgeA
    • Protein or peptide: Spore crust protein CgeA

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Supramolecule #1: Hexameric complex of Bacillus subtilis endospore crust protein CgeA

SupramoleculeName: Hexameric complex of Bacillus subtilis endospore crust protein CgeA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Molecular weightTheoretical: 84 KDa

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Macromolecule #1: Spore crust protein CgeA

MacromoleculeName: Spore crust protein CgeA / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168
Molecular weightTheoretical: 14.503417 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GAMGMSSENA QLKKDLIKAV LSPLFPTATE GGENMDSNLK ALLDACIDQK VDESETVTAE SILDPSLPAR WIFARITPGT TISIVTDSG DMIGPVVFVA FCQVHGIVFV TQESSVTPAG QATTLIDVDK VESVTFFS

UniProtKB: Spore crust protein CgeA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris buffer
150.0 mMNaClSodium chloride

Details: 20 mM Tris-HCl, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 10593 / Average electron dose: 63.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 88923
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial local fitting was done using Coot and Chimera and then PHENIX was used for flexible fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9l9d:
Bacillus subtilis endospore crust protein CgeA

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