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- PDB-8z5u: Cryo-EM structure of the rod-export apparatus with partial hook w... -

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Basic information

Entry
Database: PDB / ID: 8z5u
TitleCryo-EM structure of the rod-export apparatus with partial hook within the polar flagellar motor
Components
  • (Flagellar basal-body rod protein ...) x 3
  • (Flagellar biosynthetic protein ...) x 4
  • Flagellar M-ring protein
  • Flagellar basal body rod protein FlgB
  • Flagellar hook protein FlgE
  • Flagellar hook-basal body complex protein FliE
  • Leucine-rich repeat protein
KeywordsMOTOR PROTEIN / Polar flagellum / Polar flagellar motor / Rod
Function / homology
Function and homology information


bacterial-type flagellum basal body, distal rod / bacterial-type flagellum basal body, rod / bacterial-type flagellum basal body, MS ring / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / cytoskeletal motor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / protein targeting / plasma membrane
Similarity search - Function
Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar biosynthesis protein FliR / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Type III secretion system inner membrane R protein ...Flagellar basal-body rod FlgF / Flagellar basal-body rod FlgG / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgB / Flagellar biosynthesis protein FliR / Flagellar hook-basal body protein, FlgE/F/G / Flagellar hook-basal body protein, FlgE/F/G-like / : / Flagellar hook protein FlgE/F/G D1 domain / Type III secretion system inner membrane R protein / Bacterial export proteins, family 1 / Flagellar basal body rod protein, conserved site / Flagella basal body rod proteins signature. / Flagellar basal body rod protein, N-terminal / Flagellar basal-body/hook protein, C-terminal domain / Flagella basal body rod protein / Flagellar basal body rod FlgEFG protein C-terminal / Flagellar M-ring protein FliF / Flagellar M-ring C-terminal / Flagellar M-ring protein C-terminal / Lipoprotein YscJ/Flagellar M-ring protein / Secretory protein of YscJ/FliF family / Flagellar M-ring , N-terminal / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Flagellar basal body rod protein FlgB / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgF / Flagellar basal-body rod protein FlgG / Flagellar biosynthetic protein FliR / : / : / : / : / : ...Flagellar basal body rod protein FlgB / Flagellar basal-body rod protein FlgC / Flagellar basal-body rod protein FlgF / Flagellar basal-body rod protein FlgG / Flagellar biosynthetic protein FliR / : / : / : / : / : / : / Flagellar M-ring protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 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 rod-export apparatus with partial hook within the polar flagellar motor
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
0: Leucine-rich repeat protein
1: Flagellar biosynthetic protein FliP
2: Flagellar biosynthetic protein FliP
3: Flagellar biosynthetic protein FliP
4: Flagellar biosynthetic protein FliQ
5: Flagellar biosynthetic protein FliQ
6: Flagellar biosynthetic protein FliQ
7: Flagellar biosynthetic protein FliQ
8: Flagellar biosynthetic protein FliR
9: Leucine-rich repeat protein
A: Flagellar basal-body rod protein FlgG
AA: Flagellar M-ring protein
AB: Flagellar M-ring protein
AC: Flagellar M-ring protein
AD: Flagellar M-ring protein
AE: Flagellar M-ring protein
AF: Flagellar M-ring protein
AG: Flagellar M-ring protein
AH: Flagellar M-ring protein
AI: Flagellar M-ring protein
AJ: Flagellar M-ring protein
AK: Flagellar M-ring protein
AL: Flagellar M-ring protein
AM: Flagellar M-ring protein
AN: Flagellar M-ring protein
AO: Flagellar M-ring protein
B: Flagellar basal-body rod protein FlgG
C: Flagellar basal-body rod protein FlgG
AP: Flagellar basal-body rod protein FlgG
AQ: Flagellar basal-body rod protein FlgG
AR: Flagellar basal-body rod protein FlgG
AS: Flagellar basal-body rod protein FlgG
AT: Flagellar basal-body rod protein FlgG
AU: Flagellar basal-body rod protein FlgG
AV: Flagellar basal-body rod protein FlgG
AW: Flagellar basal-body rod protein FlgG
AX: Flagellar basal-body rod protein FlgG
AY: Flagellar basal-body rod protein FlgG
AZ: Flagellar basal-body rod protein FlgG
Aa: Flagellar basal-body rod protein FlgG
P: Flagellar basal-body rod protein FlgG
Q: Flagellar basal-body rod protein FlgG
R: Flagellar basal-body rod protein FlgG
S: Flagellar basal-body rod protein FlgG
T: Flagellar basal-body rod protein FlgG
U: Flagellar basal-body rod protein FlgG
V: Flagellar basal-body rod protein FlgG
W: Flagellar basal-body rod protein FlgG
X: Flagellar basal-body rod protein FlgG
Y: Flagellar basal-body rod protein FlgG
Z: Flagellar basal-body rod protein FlgG
a: Flagellar basal-body rod protein FlgG
b: Flagellar basal body rod protein FlgB
c: Flagellar basal body rod protein FlgB
d: Flagellar basal body rod protein FlgB
e: Flagellar basal body rod protein FlgB
f: Flagellar basal body rod protein FlgB
g: Flagellar basal-body rod protein FlgC
h: Flagellar basal-body rod protein FlgC
i: Flagellar basal-body rod protein FlgC
j: Flagellar basal-body rod protein FlgC
k: Flagellar basal-body rod protein FlgC
l: Flagellar basal-body rod protein FlgC
m: Flagellar basal-body rod protein FlgF
n: Flagellar basal-body rod protein FlgF
o: Flagellar basal-body rod protein FlgF
p: Flagellar basal-body rod protein FlgF
q: Flagellar basal-body rod protein FlgF
r: Flagellar hook-basal body complex protein FliE
s: Flagellar hook-basal body complex protein FliE
t: Flagellar hook-basal body complex protein FliE
u: Flagellar hook-basal body complex protein FliE
v: Flagellar hook-basal body complex protein FliE
w: Flagellar hook-basal body complex protein FliE
x: Flagellar biosynthetic protein FlhB
y: Flagellar biosynthetic protein FliP
z: Flagellar biosynthetic protein FliP


Theoretical massNumber of molelcules
Total (without water)2,955,34789
Polymers2,955,34789
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

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Protein , 5 types, 40 molecules DEFGHIJKLMNO09AAABACADAEAFAGAHAIAJAKALAMANAOb...

#1: Protein
Flagellar hook protein FlgE


Mass: 47434.438 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4FJD7
#2: Protein Leucine-rich repeat protein


Mass: 21518.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4FN72
#7: Protein
Flagellar M-ring protein


Mass: 63915.605 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: Q75N27
#8: Protein
Flagellar basal body rod protein FlgB


Mass: 14239.950 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0G9LZG6
#11: Protein
Flagellar hook-basal body complex protein FliE


Mass: 11135.679 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4FKP9

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Flagellar biosynthetic protein ... , 4 types, 11 molecules 123yz45678x

#3: Protein
Flagellar biosynthetic protein FliP


Mass: 31314.904 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4BDZ6
#4: Protein
Flagellar biosynthetic protein FliQ


Mass: 10329.615 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4FKL4
#5: Protein Flagellar biosynthetic protein FliR


Mass: 28905.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0H0YFV7
#12: Protein Flagellar biosynthetic protein FlhB


Mass: 42197.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4FKP7

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Flagellar basal-body rod protein ... , 3 types, 38 molecules ABCAPAQARASATAUAVAWAXAYAZAaPQRSTUVWXYZaghi...

#6: Protein ...
Flagellar basal-body rod protein FlgG / Distal rod protein


Mass: 27908.943 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0H0YB44
#9: Protein
Flagellar basal-body rod protein FlgC


Mass: 14812.569 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0G9LZH2
#10: Protein
Flagellar basal-body rod protein FlgF


Mass: 26987.387 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0G9M4M9

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Details

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
10PHENIX1.20.1_4487:model refinement
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 329955
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58418 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model

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