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- EMDB-61993: Structure of the Salmonella flagellar FliPQR complex reconstitute... -

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Basic information

Entry
Database: EMDB / ID: EMD-61993
TitleStructure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
Map data
Sample
  • Complex: Structure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ
KeywordsBacterial flagellum / flagellar assembly / electron Cryomicroscopy / type III secretion system / Salmonella / PROTEIN TRANSPORT / MOTOR PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum assembly / protein secretion / protein targeting / plasma membrane
Similarity search - Function
Flagellar biosynthesis protein FliQ / Flagellar biosynthesis protein FliR / Flagellar transport protein FliP / Type III secretion system inner membrane R protein / Bacterial export protein family 3 / Bacterial export proteins, family 1 / Bacterial export proteins, family 3 / 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 FliP / Flagellar biosynthetic protein FliR
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKinoshita M / Miyata T / Makino F / Imada K / Namba K / Minamino T
Funding support Japan, 10 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP20K15749 Japan
Japan Society for the Promotion of Science (JSPS)JP22K06162 Japan
Japan Society for the Promotion of Science (JSPS)JP19H03182 Japan
Japan Society for the Promotion of Science (JSPS)JP22H02573 Japan
Japan Society for the Promotion of Science (JSPS)JP22K19274 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP20H05532 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP22H04844 Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: A β-cap on the FliPQR protein-export channel acts as the cap for initial flagellar rod assembly.
Authors: Miki Kinoshita / Tomoko Miyata / Fumiaki Makino / Katsumi Imada / Keiichi Namba / Tohru Minamino /
Abstract: The FliPQR complex constitutes a channel for export of the flagellar proteins involved in axial structure assembly. It also serves as a template for the assembly of the rod structure, which consists ...The FliPQR complex constitutes a channel for export of the flagellar proteins involved in axial structure assembly. It also serves as a template for the assembly of the rod structure, which consists of FliE, FlgB, FlgC, FlgF, and FlgG. FliP, FliQ, and FliR assemble into a right-handed helical structure within the central pore of the flagellar basal body MS-ring, and the complex has two gates on the cytoplasmic and periplasmic sides. The periplasmic gate, formed by the N-terminal α-helices of FliP and FliR, remains closed until six FliE subunits assemble onto FliP and FliR to form the first layer of the rod, but it has remained unclear how each FliE subunit opens the gate and assembles in the absence of the rod cap required for efficient assembly of other rod proteins. Here, we present a cryoelectron microscopy structure of the FliPQR complex in closed form at 3.0 Å resolution. A β-cap, formed by the N-terminal β-strands of FliP and FliR, is located at the top of the FliPQR complex and tightly seals the closed gate. The β-cap has a narrow pore that efficiently and accurately leads the first FliE subunit to its assembly site. Interactions of FliE with FliP and FliR induce a conformational change in FliP and FliR, with their N-terminal α-helices move up and outward to open the gate. Consequently, each of the N-terminal β-strands of FliP and FliR detaches from the β-cap one after another, thereby creating a docking site for the next FliE subunit to efficiently assemble.
History
DepositionOct 17, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61993.png

Downloads & links

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Map

FileDownload / File: emd_61993.map.gz / Format: CCP4 / Size: 42.9 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 Å/pix.
x 224 pix.
= 222.88 Å		1 Å/pix.
x 224 pix.
= 222.88 Å		1 Å/pix.
x 224 pix.
= 222.88 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.995 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0117
Minimum - Maximum-0.011213656 - 0.036872372
Average (Standard dev.)0.0001440612 (±0.0016088713)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 222.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61993_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61993_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61993_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Structure of the Salmonella flagellar FliPQR complex reconstitute...

EntireName: Structure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
Components
  • Complex: Structure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
    • Protein or peptide: Flagellar biosynthetic protein FliP
    • Protein or peptide: Flagellar biosynthetic protein FliR
    • Protein or peptide: Flagellar biosynthetic protein FliQ

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Supramolecule #1: Structure of the Salmonella flagellar FliPQR complex reconstitute...

SupramoleculeName: Structure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (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 str. LT2 (bacteria)
Molecular weightTheoretical: 26.801086 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
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 str. LT2 (bacteria)
Molecular weightTheoretical: 30.320314 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
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 MPINNNPHHH HHHHHHH

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 str. LT2 (bacteria)
Molecular weightTheoretical: 9.606758 KDa
Recombinant expressionOrganism: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
SequenceString:
MTPESVMMMG TEAMKVALAL AAPLLLVALI TGLIISILQA ATQINEMTLS FIPKIVAVFI AIIVAGPWML NLLLDYVRTL FSNLPYIIG

UniProtKB: Flagellar biosynthetic protein FliQ

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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
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTristris(hydroxymethyl)aminomethane
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4885 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1015741
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109333
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 164019 / Avg.num./class: 2
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7cg4


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: 7D84
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9k29:
Structure of the Salmonella flagellar FliPQR complex reconstituted in the peptidisc

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