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- EMDB-78043: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-... -

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Basic information

Entry
Database: EMDB / ID: EMD-78043
TitleBacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin, composite
Map datacomposite full map sharpened
Sample
  • Complex: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
    • Protein or peptide: Spore germination protein A1
    • Protein or peptide: Spore germination protein A2
    • Protein or peptide: Spore germination protein A3
  • Ligand: TETRADECANE
  • Ligand: SODIUM ION
  • Ligand: ALANINE
  • Ligand: DIACYL GLYCEROL
  • Ligand: water
Keywordschannel / amino acid / LeuT / SIGNALING PROTEIN
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
Spore germination protein A1 / Spore germination protein A2 / Spore germination protein A3
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.09 Å
AuthorsCofsky JC / Kruse AC
Funding support United States, 2 items
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 JC / Kruse AC
History
DepositionJul 11, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78043.png

Downloads & links

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Map

FileDownload / File: emd_78043.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite full map sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å		0.74 Å/pix.
x 448 pix.
= 331.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-33.583396999999998 - 59.516025999999997
Average (Standard dev.)0.010764086 (±1.3056068)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: composite full map unsharpened

Fileemd_78043_additional_1.map
Annotationcomposite full map unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-...

EntireName: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
Components
  • Complex: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
    • Protein or peptide: Spore germination protein A1
    • Protein or peptide: Spore germination protein A2
    • Protein or peptide: Spore germination protein A3
  • Ligand: TETRADECANE
  • Ligand: SODIUM ION
  • Ligand: ALANINE
  • Ligand: DIACYL GLYCEROL
  • Ligand: water

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Supramolecule #1: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-...

SupramoleculeName: Bacillus subtilis GerAA:GerAB:GerAC bound to L-alanine, in glyco-diosgenin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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Macromolecule #1: Spore germination protein A1

MacromoleculeName: Spore germination protein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 56.209883 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: DYKDDDDKGS LEVLFQGPGG SGSMEQTEFK EYIHDNLALV LPKLKENDDL VKNKKMLANG LVFYYLYFSE MTDENKVSEA IKTLIKDEE TLTLDQVKKR LDQLDARPVE TAKKTIESIL NGNCAVFING LDKAYILTTG KKKTRSLTEP TTEKVVRGPK V AFVEDIDT ...String:
DYKDDDDKGS LEVLFQGPGG SGSMEQTEFK EYIHDNLALV LPKLKENDDL VKNKKMLANG LVFYYLYFSE MTDENKVSEA IKTLIKDEE TLTLDQVKKR LDQLDARPVE TAKKTIESIL NGNCAVFING LDKAYILTTG KKKTRSLTEP TTEKVVRGPK V AFVEDIDT NLALIRQRTS HPKLITKKIM IGENKLKPAA IMYIEGKAKK SVIKEVKARL KNIQLEDIQD SGTLEELIED NK YSPFPQI QNTERPDKVS SALFNGRVAI LVDSSPFVLL VPVSLGILMQ SPDDYYERWI SASLIRSLRF ASIFITLFLS SIY IALVSF HQGLLPTALA VTISANRENV PFPPIFEALL MEVTIELLRE AGLRLPNPLG QTIGLVGGVV IGQAAVEANL VSSI LVIVV SVIALASFTV PQYGMGLSFR VLRFISMFSA AILGLYGIIL FMLVVYTHLT RQTSFGSPYF SPNGFFSLKN TDDSI IRLP IKNKPKEVNN PNEPKTDSTE T

UniProtKB: Spore germination protein A1

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Macromolecule #2: Spore germination protein A2

MacromoleculeName: Spore germination protein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 41.489664 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: MSQKQTPLKL NTFQGISIVA NTMLGAGLLT LPRALTTKAN TPDGWITLIL EGFIFIFFIY LNTLIQKKHQ YPSLFEYLKE GLGKWIGSI IGLLICGYFL GVASFETRAM AEMVKFFLLE RTPIQVIILT FICCGIYLMV GGLSDVSRLF PFYLTVTIII L LIVFGISF ...String:
MSQKQTPLKL NTFQGISIVA NTMLGAGLLT LPRALTTKAN TPDGWITLIL EGFIFIFFIY LNTLIQKKHQ YPSLFEYLKE GLGKWIGSI IGLLICGYFL GVASFETRAM AEMVKFFLLE RTPIQVIILT FICCGIYLMV GGLSDVSRLF PFYLTVTIII L LIVFGISF KIFDINNLRP VLGEGLGPIA NSLTVVSISF LGMEVMLFLP EHMKKKKYTF RYASLGFLIP IILYILTYII VV GALTAPE VKTLIWPTIS LFQSFELKGI FIERFESFLL VVWIIQFFTT FVIYGYFAAN GLKKTFGLST KTSMVIIGIT VFY FSLWPD DANQVMMYSD YLGYIFVSLF LLPFILFFIV ALKRRITTK

UniProtKB: Spore germination protein A2

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Macromolecule #3: Spore germination protein A3

MacromoleculeName: Spore germination protein A3 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 40.51373 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: CWDSENIEEL SLVIGIGLDK PDDENLELTQ QILVPKIISA KEGSSSDPTQ LSITKGKTVH QMMRTSALKH KPTFSQHLRL ILLSKSVIA DQIGMDAIIN QFVRDNGTRR SSYVFITNGR TKDIFNMNDE GEPASNVIYD LTENNKVTIR TMEPVTLGEI S EHLTSDDS ...String:
CWDSENIEEL SLVIGIGLDK PDDENLELTQ QILVPKIISA KEGSSSDPTQ LSITKGKTVH QMMRTSALKH KPTFSQHLRL ILLSKSVIA DQIGMDAIIN QFVRDNGTRR SSYVFITNGR TKDIFNMNDE GEPASNVIYD LTENNKVTIR TMEPVTLGEI S EHLTSDDS FLIPHVGKEN GKLAINGASI IKNKLWHRDL TPIEVQNISL FSGTVEGGVI DLKRDGHLFS YEVYSSNRKI KT AYKDGKF KFTVTRNIEG RLSEDWNPNE DSFKDSYIKS IEKTVEKRVH ETVTSFITEK LQKEIKADVT GLGNEVRIHY PQK WKKISR KWDDDYFSNA EIDYRVNVIV RDFGTKGANK

UniProtKB: Spore germination protein A3

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Macromolecule #4: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 4 / Number of copies: 5 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #5: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 5 / Number of copies: 5
Molecular weightTheoretical: 22.99 Da

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Macromolecule #6: ALANINE

MacromoleculeName: ALANINE / type: ligand / ID: 6 / Number of copies: 5 / Formula: ALA
Molecular weightTheoretical: 89.093 Da
Chemical component information

ChemComp-ALA:
ALANINE

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Macromolecule #7: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 7 / Number of copies: 5 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 450 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration11.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.038 kPa
Details: 15 mA, 30 s glow, 10 s hold, negative, easiGlow (Pelco)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: wait time = 10 s blot time = 6 s blot force above calibrated 0 = +23.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 9093 / Average exposure time: 2.52 sec. / Average electron dose: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.6) / Number images used: 340242
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.6)

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