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- PDB-36hu: Salmonella Flagellar Export Gate with FlhB in the context of the ... -

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Basic information

Entry
Database: PDB / ID: 36hu
TitleSalmonella Flagellar Export Gate with FlhB in the context of the intact basal body
Components
  • Flagellar biosynthetic protein FlhB
  • Flagellar biosynthetic protein FliP
  • Flagellar biosynthetic protein FliQ
  • Flagellar biosynthetic protein FliR
KeywordsPROTEIN TRANSPORT / Flagella / Secretion / PMF
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 / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / 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 ...Flagellar biosynthetic protein FlhB / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / 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 biosynthetic protein FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsJohnson, S. / Johnson, M.K. / Lea, S.M.
Funding support United States, 1items
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 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A1: Flagellar biosynthetic protein FliP
B1: Flagellar biosynthetic protein FliP
C1: Flagellar biosynthetic protein FliP
D1: Flagellar biosynthetic protein FliP
E1: Flagellar biosynthetic protein FliP
F1: Flagellar biosynthetic protein FliR
G1: Flagellar biosynthetic protein FliQ
H1: Flagellar biosynthetic protein FliQ
I1: Flagellar biosynthetic protein FliQ
J1: Flagellar biosynthetic protein FliQ
K1: Flagellar biosynthetic protein FlhB


Theoretical massNumber of molelcules
Total (without water)243,77911
Polymers243,77911
Non-polymers00
Water00
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

#1: Protein
Flagellar biosynthetic protein FliP


Mass: 26801.086 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P54700
#2: Protein Flagellar biosynthetic protein FliR


Mass: 28938.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P54702
#3: Protein
Flagellar biosynthetic protein FliQ


Mass: 9606.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P0A1L5
#4: Protein Flagellar biosynthetic protein FlhB


Mass: 42407.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P40727
Has protein modificationN

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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: Focussed refinement of the Export Gate and FlhB from the intact Salmonella Flagellar Basal Body
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 58.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1SIMPLE3particle selection
2PHENIX2.0_5936model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151443 / Symmetry type: POINT
RefinementCross valid method: NONE

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