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- EMDB-77603: Salmonella Flagellar Export Apparatus (FliPQR/FlhB/FlhA) in the c... -

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Basic information

Entry
Database: EMDB / ID: EMD-77603
TitleSalmonella Flagellar Export Apparatus (FliPQR/FlhB/FlhA) in the context of the intact basal body
Map data
Sample
  • Complex: Focussed refinement of the Export Apparatus (FliPQR/FlhB/FlhA) from the intact Salmonella Flagellar Basal Body
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar biosynthetic protein FlhB
    • Protein or peptide: Flagellar biosynthesis protein FlhA
KeywordsFlagella / Secretion / PMF / PROTEIN TRANSPORT
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / protein secretion / bacterial-type flagellum assembly / protein targeting / plasma membrane
Similarity search - Function
Flagellar biosynthetic protein FlhB / Flagellar biosynthesis protein FlhA / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FHIPEP, domain 3 / FHIPEP, domain 4 ...Flagellar biosynthetic protein FlhB / Flagellar biosynthesis protein FlhA / FHIPEP, domain 1 / FHIPEP conserved site / Bacterial export FHIPEP family signature. / Type III secretion system FHIPEP / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FHIPEP, domain 3 / FHIPEP, domain 4 / FHIPEP family / FlhB HrpN YscU SpaS Family / Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Bacterial export protein family 3 / Bacterial export proteins, family 3 / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1 / Flagella transport protein fliP family signature 1. / Type III secretion system inner membrane P protein / FliP family / Flagella transport protein fliP family signature 2.
Similarity search - Domain/homology
Flagellar biosynthetic protein FliQ / Flagellar biosynthetic protein FlhB / Flagellar biosynthesis protein FlhA / Flagellar biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsJohnson S / Johnson MK / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: bioRxiv / Year: 2026
Title: Structure of the proton-powered secretion motor at the heart of the bacterial flagellum.
Authors: Mary K Johnson / Steven Johnson / Justin C Deme / Luz Alfaro-Alvarado / Owain J Bryant / Fabienne F V Chevance / Kelly T Hughes / Susan M Lea /
Abstract: Bacterial type III secretion systems export proteins across the inner membrane using the proton-motive force (PMF), but how proton flow is coupled to opening of the export channel is unknown. Here we ...Bacterial type III secretion systems export proteins across the inner membrane using the proton-motive force (PMF), but how proton flow is coupled to opening of the export channel is unknown. Here we present single-particle cryo-EM structures at 2.5-4.2 Å resolution of the intact flagellar Export Apparatus from , obtained using optimized extraction conditions of the endogenous assembly that retain the complete transmembrane complex. The transmembrane domain of FlhA forms a nonameric funnel-shaped basket beneath the Export Gate, with each subunit harboring a buried pathway of conserved hydrophilic residues spanning the hydrophobic core of the membrane. FlhB is resolved for the first time within the intact gate, revealing helices that thread through the FlhA channel, completely sealing it at rest. A symmetry-free reconstruction captures one FlhA protomer hinged outward at the water-filled cavity, breaking the rotational symmetry. Together, these structures define the architecture of the proton-transducing element of the type III secretion system and suggest a rotary gating mechanism, with parallels to the F motor of ATP synthase, in which PMF-driven conformational cycling of FlhA drives regulated opening of the export channel.
History
DepositionJun 11, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77603.png

Downloads & links

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Map

FileDownload / File: emd_77603.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.11290933 - 12.234991000000001
Average (Standard dev.)0.018146954 (±0.3753937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_77603_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_77603_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 : Focussed refinement of the Export Apparatus (FliPQR/FlhB/FlhA) fr...

EntireName: Focussed refinement of the Export Apparatus (FliPQR/FlhB/FlhA) from the intact Salmonella Flagellar Basal Body
Components
  • Complex: Focussed refinement of the Export Apparatus (FliPQR/FlhB/FlhA) from the intact Salmonella Flagellar Basal Body
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
    • Protein or peptide: Flagellar biosynthetic protein FlhB
    • Protein or peptide: Flagellar biosynthesis protein FlhA

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Supramolecule #1: Focussed refinement of the Export Apparatus (FliPQR/FlhB/FlhA) fr...

SupramoleculeName: Focussed refinement of the Export Apparatus (FliPQR/FlhB/FlhA) from the intact Salmonella Flagellar Basal Body
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #1: Flagellar biosynthetic protein FliP

MacromoleculeName: Flagellar biosynthetic protein FliP / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 26.801086 KDa
SequenceString: MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ...String:
MRRLLFLSLA GLWLFSPAAA AQLPGLISQP LAGGGQSWSL SVQTLVFITS LTFLPAILLM MTSFTRIIIV FGLLRNALGT PSAPPNQVL LGLALFLTFF IMSPVIDKIY VDAYQPFSEQ KISMQEALDK GAQPLRAFML RQTREADLAL FARLANSGPL Q GPEAVPMR ILLPAYVTSE LKTAFQIGFT IFIPFLIIDL VIASVLMALG MMMVPPATIA LPFKLMLFVL VDGWQLLMGS LA QSFYS

UniProtKB: Flagellar biosynthetic protein FliP

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Macromolecule #2: Flagellar biosynthetic protein FliR

MacromoleculeName: Flagellar biosynthetic protein FliR / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 28.938865 KDa
SequenceString: MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA ...String:
MIQVTSEQWL YWLHLYFWPL LRVLALISTA PILSERAIPK RVKLGLGIMI TLVIAPSLPA NDTPLFSIAA LWLAMQQILI GIALGFTMQ FAFAAVRTAG EFIGLQMGLS FATFVDPGSH LNMPVLARIM DMLAMLLFLT FNGHLWLISL LVDTFHTLPI G SNPVNSNA FMALARAGGL IFLNGLMLAL PVITLLLTLN LALGLLNRMA PQLSIFVIGF PLTLTVGIML MAALMPLIAP FC EHLFSEI FNLLADIVSE MPINNNP

UniProtKB: Flagellar biosynthetic protein FliR

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Macromolecule #3: Flagellar biosynthetic protein FliQ

MacromoleculeName: Flagellar biosynthetic protein FliQ / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 9.606758 KDa
SequenceString:
MTPESVMMMG TEAMKVALAL AAPLLLVALI TGLIISILQA ATQINEMTLS FIPKIVAVFI AIIVAGPWML NLLLDYVRTL FSNLPYIIG

UniProtKB: Flagellar biosynthetic protein FliQ

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Macromolecule #4: Flagellar biosynthetic protein FlhB

MacromoleculeName: Flagellar biosynthetic protein FlhB / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 42.407879 KDa
SequenceString: MAEESDDDKT EAPTPHRLEK AREEGQIPRS RELTSLLILL VGVCIIWFGG ESLARQLAGM LSAGLHFDHR MVNDPNLILG QIILLIKAA MMALLPLIAG VVLVALISPV MLGGLIFSGK SLQPKFSKLN PLPGIKRMFS AQTGAELLKA VLKSTLVGCV T GFYLWHHW ...String:
MAEESDDDKT EAPTPHRLEK AREEGQIPRS RELTSLLILL VGVCIIWFGG ESLARQLAGM LSAGLHFDHR MVNDPNLILG QIILLIKAA MMALLPLIAG VVLVALISPV MLGGLIFSGK SLQPKFSKLN PLPGIKRMFS AQTGAELLKA VLKSTLVGCV T GFYLWHHW PQMMRLMAES PIVAMGNALD LVGLCALLVV LGVIPMVGFD VFFQIFSHLK KLRMSRQDIR DEFKESEGDP HV KGKIRQM QRAAAQRRMM EDVPKADVIV TNPTHYSVAL QYDENKMSAP KVVAKGAGLI ALRIREIGAE HRVPTLEAPP LAR ALYRHA EIGQQIPGQL YAAVAEVLAW VWQLKRWRLA GGQRPPQPEN LPVPEALDFM NEKNTDG

UniProtKB: Flagellar biosynthetic protein FlhB

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Macromolecule #5: Flagellar biosynthesis protein FlhA

MacromoleculeName: Flagellar biosynthesis protein FlhA / type: protein_or_peptide / ID: 5 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Molecular weightTheoretical: 74.913484 KDa
SequenceString: MANLVAMLRL PSNLKSTQWQ ILAGPILILL ILSMMVLPLP AFILDLLFTF NIALSIMVLL VAMFTQRTLD FAAFPTILLF TTLLRLALN VASTRIILME GHTGAAAAGK VVEAFGHFLV GGNFAIGIVV FIILVIINFM VITKGAGRIA EVGARFVLDG M PGKQMAID ...String:
MANLVAMLRL PSNLKSTQWQ ILAGPILILL ILSMMVLPLP AFILDLLFTF NIALSIMVLL VAMFTQRTLD FAAFPTILLF TTLLRLALN VASTRIILME GHTGAAAAGK VVEAFGHFLV GGNFAIGIVV FIILVIINFM VITKGAGRIA EVGARFVLDG M PGKQMAID ADLNAGLIGE DEAKKRRSEV TQEADFYGSM DGASKFVRGD AIAGILIMVI NVVGGLLVGV LQHGMSIGSA AE SYTLLTI GDGLVAQIPA LVISTAAGVI VTRVSTDQDV GEQMVGQLFS NPRVMLLAAA VLGLLGMVPG MPNLVFLLFT AAL LGLAWW LRGREEKAPE EPQPVKMPEN NSVVEATWND VQLEDSLGME VGYRLIPMVD FQQDGELLGR IRSIRKKFAQ DMGF LPPVV HIRDNMDLQP ARYRILMKGV EIGSGDAYPG RWLAINPGTA AGTLPGEKTV DPAFGLDAIW IESALKEQAQ IQGFT VVEA STVVATHLNH LIGQFSAELF GRQEAQQLLD RVSQEMPKLT EDLVPGVVTL TTLHKVLQNL LAEKVPIRDM RTILET LAE HAPLQSDPHE LTAVVRVALG RAITQQWFPG NEEVQVIGLD TALERLLLQA LQGGGGLEPG LADRLLAQTQ EALSRQE ML GAPPVLLVNH ALRPLLSRFL RRSLPQLVVL SNLELSDNRH IRMTATIGGK

UniProtKB: Flagellar biosynthesis protein FlhA

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 58.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
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: OTHER / Details: Ab Initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 58082
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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