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- EMDB-78037: Bacillus subtilis GerAA:GerAB:GerAC, in glyco-diosgenin, consensus -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-78037
TitleBacillus subtilis GerAA:GerAB:GerAC, in glyco-diosgenin, consensus
Map dataconsensus reconstruction, full map sharpened
Sample
  • Complex: Bacillus subtilis GerAA:GerAB:GerAC, in glyco-diosgenin
    • Protein or peptide: GerAA
    • Protein or peptide: GerAB
    • Protein or peptide: GerAC
Keywordschannel / amino acid / LeuT / SIGNALING PROTEIN
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.02 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_78037.png

Downloads & links

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Map

FileDownload / File: emd_78037.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus reconstruction, 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: 0.08
Minimum - Maximum-0.50959545 - 0.672374
Average (Standard dev.)0.00015164254 (±0.012966774)
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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Mask #1

Fileemd_78037_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_78037_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: consensus reconstruction, full map unsharpened

Fileemd_78037_additional_1.map
Annotationconsensus reconstruction, full map unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: consensus reconstruction, half map 2

Fileemd_78037_half_map_1.map
Annotationconsensus reconstruction, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: consensus reconstruction, half map 1

Fileemd_78037_half_map_2.map
Annotationconsensus reconstruction, half map 1
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, in glyco-diosgenin

EntireName: Bacillus subtilis GerAA:GerAB:GerAC, in glyco-diosgenin
Components
  • Complex: Bacillus subtilis GerAA:GerAB:GerAC, in glyco-diosgenin
    • Protein or peptide: GerAA
    • Protein or peptide: GerAB
    • Protein or peptide: GerAC

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Supramolecule #1: Bacillus subtilis GerAA:GerAB:GerAC, in glyco-diosgenin

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

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Macromolecule #1: GerAA

MacromoleculeName: GerAA / 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

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Macromolecule #2: GerAB

MacromoleculeName: GerAB / 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

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Macromolecule #3: GerAC

MacromoleculeName: GerAC / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 40.728977 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: (LIG)CWDSENIEE LSLVIGIGLD KPDDENLELT QQILVPKIIS AKEGSSSDPT QLSITKGKTV HQMMRTSALK HKPTFS QHL RLILLSKSVI ADQIGMDAII NQFVRDNGTR RSSYVFITNG RTKDIFNMND EGEPASNVIY DLTENNKVTI RTMEPVT LG EISEHLTSDD ...String:
(LIG)CWDSENIEE LSLVIGIGLD KPDDENLELT QQILVPKIIS AKEGSSSDPT QLSITKGKTV HQMMRTSALK HKPTFS QHL RLILLSKSVI ADQIGMDAII NQFVRDNGTR RSSYVFITNG RTKDIFNMND EGEPASNVIY DLTENNKVTI RTMEPVT LG EISEHLTSDD SFLIPHVGKE NGKLAINGAS IIKNKLWHRD LTPIEVQNIS LFSGTVEGGV IDLKRDGHLF SYEVYSSN R KIKTAYKDGK FKFTVTRNIE GRLSEDWNPN EDSFKDSYIK SIEKTVEKRV HETVTSFITE KLQKEIKADV TGLGNEVRI HYPQKWKKIS RKWDDDYFSN AEIDYRVNVI VRDFGTKGAN K

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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
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: 10900 / Average exposure time: 2.46 sec. / Average electron dose: 50.3 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: NONE / Details: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.6) / Number images used: 259371
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.6)
FSC plot (resolution estimation)

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