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- PDB-8z5n: Cryo-EM structure of the LPHT ring -

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Basic information

Entry
Database: PDB / ID: 8z5n
TitleCryo-EM structure of the LPHT ring
Components
  • Component of sodium-driven polar flagellar motor
  • Flagella basal-body protein
  • Flagellar L-ring protein
  • Flagellar P-ring protein
  • Flagellar assembly lipoprotein FlgP
  • Sodium-type flagellar motor component
  • The N-terminus of Flagellar L-ring protein
KeywordsMOTOR PROTEIN / Polar flagellum / Polar flagellar motor / LPHT ring / Bushing
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / MotY N-terminal domain / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / MotY N-terminal domain / Flagellar protein FlgP ...Flagellar assembly protein T, N-terminal / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, C-terminal / FlgT, C-terminal domain superfamily / MotY N-terminal domain / Flagellar assembly protein T, C-terminal domain / Flagellar assembly protein T, middle domain / Flagellar assembly protein T, N-terminal domain / MotY N-terminal domain / Flagellar protein FlgP / : / FlgT, N-terminal domain superfamily / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Sel1 repeat / Sel1-like repeat / Sel1-like repeats. / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Flagellar assembly lipoprotein FlgP / : / : / Flagella basal-body protein / Component of sodium-driven polar flagellar motor / Sodium-type flagellar motor component
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 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 LPHT ring
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
A: Component of sodium-driven polar flagellar motor
B: Component of sodium-driven polar flagellar motor
C: Sodium-type flagellar motor component
D: Sodium-type flagellar motor component
E: Component of sodium-driven polar flagellar motor
F: Component of sodium-driven polar flagellar motor
G: Sodium-type flagellar motor component
H: Sodium-type flagellar motor component
I: Component of sodium-driven polar flagellar motor
J: Component of sodium-driven polar flagellar motor
K: Sodium-type flagellar motor component
L: Sodium-type flagellar motor component
M: Component of sodium-driven polar flagellar motor
N: Component of sodium-driven polar flagellar motor
O: Sodium-type flagellar motor component
P: Sodium-type flagellar motor component
Q: Component of sodium-driven polar flagellar motor
R: Component of sodium-driven polar flagellar motor
S: Sodium-type flagellar motor component
T: Sodium-type flagellar motor component
U: Component of sodium-driven polar flagellar motor
V: Component of sodium-driven polar flagellar motor
W: Sodium-type flagellar motor component
X: Sodium-type flagellar motor component
Y: Component of sodium-driven polar flagellar motor
Z: Component of sodium-driven polar flagellar motor
a: Sodium-type flagellar motor component
b: Sodium-type flagellar motor component
c: Component of sodium-driven polar flagellar motor
d: Component of sodium-driven polar flagellar motor
e: Sodium-type flagellar motor component
f: Sodium-type flagellar motor component
g: Component of sodium-driven polar flagellar motor
h: Component of sodium-driven polar flagellar motor
i: Sodium-type flagellar motor component
j: Sodium-type flagellar motor component
k: Component of sodium-driven polar flagellar motor
l: Component of sodium-driven polar flagellar motor
m: Sodium-type flagellar motor component
n: Sodium-type flagellar motor component
o: Component of sodium-driven polar flagellar motor
p: Component of sodium-driven polar flagellar motor
q: Sodium-type flagellar motor component
r: Sodium-type flagellar motor component
s: Component of sodium-driven polar flagellar motor
t: Component of sodium-driven polar flagellar motor
u: Sodium-type flagellar motor component
v: Sodium-type flagellar motor component
w: Component of sodium-driven polar flagellar motor
x: Component of sodium-driven polar flagellar motor
y: Sodium-type flagellar motor component
z: Sodium-type flagellar motor component
1: Flagellar L-ring protein
2: Flagellar assembly lipoprotein FlgP
3: The N-terminus of Flagellar L-ring protein
4: Flagellar P-ring protein
5: Flagella basal-body protein
6: Flagellar L-ring protein
7: Flagellar assembly lipoprotein FlgP
8: The N-terminus of Flagellar L-ring protein
9: Flagellar P-ring protein
0: Flagella basal-body protein
AA: Flagellar L-ring protein
AB: Flagellar assembly lipoprotein FlgP
AC: The N-terminus of Flagellar L-ring protein
AD: Flagellar P-ring protein
AE: Flagella basal-body protein
AF: Flagellar L-ring protein
AG: Flagellar assembly lipoprotein FlgP
AH: The N-terminus of Flagellar L-ring protein
AI: Flagellar P-ring protein
AJ: Flagella basal-body protein
AK: Flagellar L-ring protein
AL: Flagellar assembly lipoprotein FlgP
AM: The N-terminus of Flagellar L-ring protein
AN: Flagellar P-ring protein
AO: Flagella basal-body protein
AP: Flagellar L-ring protein
AQ: Flagellar assembly lipoprotein FlgP
AR: The N-terminus of Flagellar L-ring protein
AS: Flagellar P-ring protein
AT: Flagella basal-body protein
AU: Flagellar L-ring protein
AV: Flagellar assembly lipoprotein FlgP
AW: The N-terminus of Flagellar L-ring protein
AX: Flagellar P-ring protein
AY: Flagella basal-body protein
AZ: Flagellar L-ring protein
Aa: Flagellar assembly lipoprotein FlgP
Ab: The N-terminus of Flagellar L-ring protein
Ac: Flagellar P-ring protein
Ad: Flagella basal-body protein
Ae: Flagellar L-ring protein
Af: Flagellar assembly lipoprotein FlgP
Ag: The N-terminus of Flagellar L-ring protein
Ah: Flagellar P-ring protein
Ai: Flagella basal-body protein
Aj: Flagellar L-ring protein
Ak: Flagellar assembly lipoprotein FlgP
Al: The N-terminus of Flagellar L-ring protein
Am: Flagellar P-ring protein
An: Flagella basal-body protein
Ao: Flagellar L-ring protein
Ap: Flagellar assembly lipoprotein FlgP
Aq: The N-terminus of Flagellar L-ring protein
Ar: Flagellar P-ring protein
As: Flagella basal-body protein
At: Flagellar L-ring protein
Au: Flagellar assembly lipoprotein FlgP
Av: The N-terminus of Flagellar L-ring protein
Aw: Flagellar P-ring protein
Ax: Flagella basal-body protein
Ay: Flagellar L-ring protein
Az: Flagellar assembly lipoprotein FlgP
A1: The N-terminus of Flagellar L-ring protein
A2: Flagellar P-ring protein
A3: Flagella basal-body protein
A4: Flagellar L-ring protein
A5: Flagellar assembly lipoprotein FlgP
A6: The N-terminus of Flagellar L-ring protein
A7: Flagellar P-ring protein
A8: Flagella basal-body protein
A9: Flagellar L-ring protein
A0: Flagellar assembly lipoprotein FlgP
BA: The N-terminus of Flagellar L-ring protein
BB: Flagellar P-ring protein
BC: Flagella basal-body protein
BD: Flagellar L-ring protein
BE: Flagellar assembly lipoprotein FlgP
BF: The N-terminus of Flagellar L-ring protein
BG: Flagellar P-ring protein
BH: Flagella basal-body protein
BI: Flagellar L-ring protein
BJ: Flagellar assembly lipoprotein FlgP
BK: The N-terminus of Flagellar L-ring protein
BL: Flagellar P-ring protein
BM: Flagella basal-body protein
BN: Flagellar L-ring protein
BO: Flagellar assembly lipoprotein FlgP
BP: The N-terminus of Flagellar L-ring protein
BQ: Flagellar P-ring protein
BR: Flagella basal-body protein
BS: Flagellar L-ring protein
BT: Flagellar assembly lipoprotein FlgP
BU: The N-terminus of Flagellar L-ring protein
BV: Flagellar P-ring protein
BW: Flagella basal-body protein
BX: Flagellar L-ring protein
BY: Flagellar assembly lipoprotein FlgP
BZ: The N-terminus of Flagellar L-ring protein
Ba: Flagellar P-ring protein
Bb: Flagella basal-body protein
Bc: Flagellar L-ring protein
Bd: Flagellar assembly lipoprotein FlgP
Be: The N-terminus of Flagellar L-ring protein
Bf: Flagellar P-ring protein
Bg: Flagella basal-body protein
Bh: Flagellar L-ring protein
Bi: Flagellar assembly lipoprotein FlgP
Bj: The N-terminus of Flagellar L-ring protein
Bk: Flagellar P-ring protein
Bl: Flagella basal-body protein
Bm: Flagellar L-ring protein
Bn: Flagellar assembly lipoprotein FlgP
Bo: The N-terminus of Flagellar L-ring protein
Bp: Flagellar P-ring protein
Bq: Flagella basal-body protein
Br: Flagellar L-ring protein
Bs: Flagellar assembly lipoprotein FlgP
Bt: The N-terminus of Flagellar L-ring protein
Bu: Flagellar P-ring protein
Bv: Flagella basal-body protein
Bw: Flagellar L-ring protein
Bx: Flagellar assembly lipoprotein FlgP
By: The N-terminus of Flagellar L-ring protein
Bz: Flagellar P-ring protein
B1: Flagella basal-body protein
B2: Flagellar L-ring protein
B3: Flagellar assembly lipoprotein FlgP
B4: The N-terminus of Flagellar L-ring protein
B5: Flagellar P-ring protein
B6: Flagella basal-body protein


Theoretical massNumber of molelcules
Total (without water)4,773,869182
Polymers4,773,869182
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 , 6 types, 156 molecules ABEFIJMNQRUVYZcdghklopstwxCDGH...

#1: Protein ...
Component of sodium-driven polar flagellar motor / Sodium-type flagellar protein MotY


Mass: 33528.008 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: P74944
#2: Protein ...
Sodium-type flagellar motor component / Sodium-type polar flagellar protein MotX


Mass: 24088.613 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: Q93R25
#3: Protein ...
Flagellar L-ring protein / Basal body L-ring protein


Mass: 27929.951 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4BB53
#4: Protein ...
Flagellar assembly lipoprotein FlgP / Flagellar biosynthesis protein FlgP


Mass: 16303.760 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A0H0Y943
#6: Protein ...
Flagellar P-ring protein / Basal body P-ring protein


Mass: 37892.234 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: A0A9W4BSQ4
#7: Protein ...
Flagella basal-body protein


Mass: 42417.168 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148 / References: UniProt: D9N551

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Protein/peptide , 1 types, 26 molecules 38ACAHAMARAWAbAgAlAqAvA1A6BABFBKBPBUBZBeBjBoBtByB4

#5: Protein/peptide ...
The N-terminus of Flagellar L-ring protein


Mass: 1450.630 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Vibrio alginolyticus (bacteria) / Strain: KK148

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Details

Has protein modificationY

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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
SymmetryPoint symmetry: C13 (13 fold cyclic)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45233 / 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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