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- EMDB-39788: Cryo-EM structure of the L-hook of the polar flagellum -

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Basic information

Entry
Database: EMDB / ID: EMD-39788
TitleCryo-EM structure of the L-hook of the polar flagellum
Map dataMain map
Sample
  • Complex: The polar flagellar motor-hook complex
    • Protein or peptide: Flagellar hook protein FlgE
KeywordsPolar flagellum / Polar flagellar motor / Hook / MOTOR PROTEIN
Function / homology:
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsZhang L / Tan JX / Zhou Y / Zhu YQ
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81925024 China
National Natural Science Foundation of China (NSFC)U23A20163 China
Ministry of Science and Technology (MoST, China)2017YFA0503900 China
CitationJournal: Protein Cell / Year: 2026
Title: Molecular basis of high-torque transmission of the Vibrio polar flagellar motor.
Authors: Ling Zhang / Jiaxing Tan / Xuemin Duan / Xiaofei Wang / Ting Wang / Keke Yuan / Michio Homma / Seiji Kojima / Yan Zhou / Yongqun Zhu /
Abstract: The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission ...The bacterial flagellar motor is a protein nanomachine that rotates the flagellum to facilitate bacterial motility. These motors exhibit structural diversity among species, enabling the transmission of varying torques to flagellar filaments to grant bacteria diverse swimming capabilities. Compared to peritrichous flagellar motors, polar flagellar motors are faster machines that transmit higher torque to drive high-speed motility in liquids and empower swimming in viscous environments. However, structural basis of high-torque transmission of the polar flagellar motors is still unclear. Here we present a cryo-electron microscopy structure of the polar flagellar motor in complex with the hook from Vibrio alginolyticus, comprising 295 subunits from 18 proteins. Compared to the peritrichous flagellar rod, this structure reveals an increased number of inter-subunit interactions in the rod of the polar flagellar motor. Nine phospholipid molecules insert into the interface between the export apparatus and the proximal rod. The LP ring contains more electrostatic charges on the inner surface and has fewer physical contacts with the rod, while the HT ring tightly binds to the outer surface of the LP ring. FlrP, a protein of previously unknown function, is identified as a new component of the polar flagellar motor, and extensively participates in the interactions of 15 FliF peptides of the MS ring with the rod. In contrast to that in the peritrichous flagellum, the hook in the polar flagellum has two different conformational states, L- and R-types. These findings provide unprecedented insights into structural adaptations of the bacterial polar flagellar motors for high-torque transmission.
History
DepositionApr 18, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39788.png

Downloads & links

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Map

FileDownload / File: emd_39788.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 380 pix.
= 456. Å		1.2 Å/pix.
x 380 pix.
= 456. Å		1.2 Å/pix.
x 380 pix.
= 456. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.2225052 - 1.813556
Average (Standard dev.)0.0019075422 (±0.08776765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 456.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_39788_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_39788_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The polar flagellar motor-hook complex

EntireName: The polar flagellar motor-hook complex
Components
  • Complex: The polar flagellar motor-hook complex
    • Protein or peptide: Flagellar hook protein FlgE

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Supramolecule #1: The polar flagellar motor-hook complex

SupramoleculeName: The polar flagellar motor-hook complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148

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Macromolecule #1: Flagellar hook protein FlgE

MacromoleculeName: Flagellar hook protein FlgE / type: protein_or_peptide / ID: 1 / Number of copies: 40 / Enantiomer: LEVO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Molecular weightTheoretical: 47.434438 KDa
SequenceString: MSYVSLSGLS AAQLDLNTTS NNIANANTYG FKESRAEFAD VYSNSLFTNA KTTPGGGAQA SQVAQQFHEG SSIYTNNPMD LRVSGTGFF AVAKERLTPQ QNELTRNGAF HLNKENYMVT ANDEFLLGYQ VDPSSGEVSS YEPQPINIPA EFGKPKQTAN I EVGVNLPA ...String:
MSYVSLSGLS AAQLDLNTTS NNIANANTYG FKESRAEFAD VYSNSLFTNA KTTPGGGAQA SQVAQQFHEG SSIYTNNPMD LRVSGTGFF AVAKERLTPQ QNELTRNGAF HLNKENYMVT ANDEFLLGYQ VDPSSGEVSS YEPQPINIPA EFGKPKQTAN I EVGVNLPA NGDLKDPTQF DFSDPDTYNR STSSTIYDSM GQSYKLTTYY LKDQTQPNTW NTYYTVTDKE GEKPLNVAAG DA QTPTGHV GHTMKFNNDG TLASLNNGQP ITSVALGDPA TNTTPVDMNG ADPAQTLNFG LGSATQFAAP FELTKFDEDG ATT GFLTKV DFDENGSVMG TYSNGENVTL GRVALVRVPN EQGLDKKGGT QWDSTQFSGD KIWGESNKGS FGTINNGMLE QSNI DMTQE LVDLISAQRN FQANSRSLEV HNQLQQNILQ IR

UniProtKB: UNIPROTKB: A0A9W4FJD7

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 329955
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 32950
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8z5y:
Cryo-EM structure of the L-hook of the polar flagellum

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