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- PDB-37br: Bacillus subtilis GerAA(A318C):GerAB:GerAC(S56C) bound to D-alani... -

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Basic information

Entry
Database: PDB / ID: 37br
TitleBacillus subtilis GerAA(A318C):GerAB:GerAC(S56C) bound to D-alanine, in glyco-diosgenin
Components(Spore germination protein ...) x 3
KeywordsSIGNALING PROTEIN / channel / amino acid / LeuT
Function / homology
Function and homology information


spore germination / plasma membrane
Similarity search - Function
Spore germination GerAB / Spore germination protein / Spore germination GerAC / Spore germination GerAC, C-terminal domain superfamily / : / : / Spore germination B3/ GerAC like, C-terminal / Spore germination protein N-terminal domain / Bacillus/Clostridium Ger spore germination protein / Bacillus/Clostridium GerA spore germination protein ...Spore germination GerAB / Spore germination protein / Spore germination GerAC / Spore germination GerAC, C-terminal domain superfamily / : / : / Spore germination B3/ GerAC like, C-terminal / Spore germination protein N-terminal domain / Bacillus/Clostridium Ger spore germination protein / Bacillus/Clostridium GerA spore germination protein / : / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
TETRADECANE / D-ALANINE / DIACYL GLYCEROL / Spore germination protein A1 / Spore germination protein A2 / Spore germination protein A3
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å
AuthorsCofsky, J.C. / Kruse, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI164647 United States
Helen Hay Whitney Foundation United States
CitationJournal: To Be Published
Title: Bacterial spore nutrient receptors repurpose an ancient transporter as a germination trigger switch
Authors: Cofsky, J.C. / Kruse, A.C.
History
DepositionJul 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spore germination protein A1
B: Spore germination protein A2
C: Spore germination protein A3
E: Spore germination protein A1
F: Spore germination protein A2
G: Spore germination protein A3
I: Spore germination protein A1
J: Spore germination protein A2
K: Spore germination protein A3
M: Spore germination protein A1
N: Spore germination protein A2
O: Spore germination protein A3
Q: Spore germination protein A1
R: Spore germination protein A2
S: Spore germination protein A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)695,98435
Polymers691,30715
Non-polymers4,67720
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Spore germination protein ... , 3 types, 15 molecules AEIMQBFJNRCGKOS

#1: Protein
Spore germination protein A1


Mass: 56241.945 Da / Num. of mol.: 5 / Mutation: A318C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: gerAA, gerA1, BSU33050
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain (production host): bJCC_353 / References: UniProt: P07868
#2: Protein
Spore germination protein A2


Mass: 41489.664 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: gerAB, gerA2, BSU33060
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain (production host): bJCC_353 / References: UniProt: P07869
#3: Protein
Spore germination protein A3


Mass: 40529.793 Da / Num. of mol.: 5 / Mutation: S56C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: gerAC, gerA3, BSU33070
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P07870

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Non-polymers , 5 types, 730 molecules

#4: Chemical
ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C39H76O5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bacillus subtilis GerAA(A318C):GerAB:GerAC(S56C) bound to D-alanine, in glyco-diosgenin
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (recombinant)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: bJCC_353
Buffer solutionpH: 7.5
SpecimenConc.: 11.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA, 30 s glow, 10 s hold, negative, easiGlow (Pelco)
Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: wait time = 10 s blot time = 6 s blot force above calibrated 0 = +23

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Image recordingAverage exposure time: 2.46 sec. / Electron dose: 50.3 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10500

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5.0.6particle selection
2EPUimage acquisition
4cryoSPARC5.0.6CTF correction
9PHENIX2.1model refinement
10Coot1.3.1model refinement
11cryoSPARC5.0.6initial Euler assignment
12cryoSPARC5.0.6final Euler assignment
14cryoSPARC5.0.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325035 / Symmetry type: POINT

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