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

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Basic information

Entry
Database: PDB / ID: 8z5y
TitleCryo-EM structure of the L-hook of the polar flagellum
ComponentsFlagellar hook protein FlgE
KeywordsMOTOR PROTEIN / Polar flagellum / Polar flagellar motor / Hook
Function / homology:
Function and homology information
Biological speciesVibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsZhang, L. / Tan, J.X. / Zhou, Y. / Zhu, Y.Q.
Funding support China, 3items
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: To Be Published
Title: Cryo-EM structure of the L-hook of the polar flagellum
Authors: Zhang, L. / Tan, J.X. / Zhou, Y. / Zhu, Y.Q.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Flagellar hook protein FlgE
E: Flagellar hook protein FlgE
F: Flagellar hook protein FlgE
G: Flagellar hook protein FlgE
H: Flagellar hook protein FlgE
I: Flagellar hook protein FlgE
J: Flagellar hook protein FlgE
K: Flagellar hook protein FlgE
L: Flagellar hook protein FlgE
M: Flagellar hook protein FlgE
N: Flagellar hook protein FlgE
O: Flagellar hook protein FlgE
P: Flagellar hook protein FlgE
Q: Flagellar hook protein FlgE
R: Flagellar hook protein FlgE
S: Flagellar hook protein FlgE
T: Flagellar hook protein FlgE
U: Flagellar hook protein FlgE
V: Flagellar hook protein FlgE
W: Flagellar hook protein FlgE
X: Flagellar hook protein FlgE
Y: Flagellar hook protein FlgE
Z: Flagellar hook protein FlgE
a: Flagellar hook protein FlgE
b: Flagellar hook protein FlgE
c: Flagellar hook protein FlgE
d: Flagellar hook protein FlgE
e: Flagellar hook protein FlgE
f: Flagellar hook protein FlgE
g: Flagellar hook protein FlgE
h: Flagellar hook protein FlgE
i: Flagellar hook protein FlgE
j: Flagellar hook protein FlgE
k: Flagellar hook protein FlgE
l: Flagellar hook protein FlgE
m: Flagellar hook protein FlgE
n: Flagellar hook protein FlgE
o: Flagellar hook protein FlgE
p: Flagellar hook protein FlgE
q: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)1,897,37840
Polymers1,897,37840
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellar hook protein FlgE


Mass: 47434.438 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4FJD7
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: The polar flagellar motor-hook complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vibrio alginolyticus (bacteria) / Strain: KK148
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
8UCSF ChimeraXmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 329955
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32950 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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