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- PDB-9go6: Salmonella hook-filament junction complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9go6
TitleSalmonella hook-filament junction complex
Components
  • Flagellar hook protein FlgE
  • Flagellar hook-associated protein
  • Flagellar hook-associated protein 1
  • Flagellin
KeywordsTRANSPORT PROTEIN / Bacterial flagellum / Hook-filament junction / FlgK / FlgL / Salmonella enterica
Function / homology
Function and homology information


bacterial-type flagellum hook / bacterial-type flagellum basal body / bacterial-type flagellum-dependent swarming motility / bacterial-type flagellum / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / cytosol
Similarity search - Function
: / Flagellar hook-associated protein 1, D2-like domain / Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 3 / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain ...: / Flagellar hook-associated protein 1, D2-like domain / Flagellar hook-associated protein 1 / : / Flagellar hook-associated protein FlgK helical domain / Flagellar hook-associated protein 3 / Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / Flagellar hook protein FlgE superfamily / Flagellar hook protein FlgE / Flagellar basal body protein FlaE D2 domain / 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 / Flagellin, C-terminal domain, subdomain 2 / 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 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellar hook-associated protein / Flagellar hook protein FlgE / Flagellar hook-associated protein 1 / Flagellin
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQin, K. / Einenkel, R. / Erhardt, E. / Bergeron, J.R.
Funding support United Kingdom, France, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R009759/2 United Kingdom
Human Frontier Science Program (HFSP)RGY0080/2021 France
CitationJournal: To Be Published
Title: Structure of the complete extracellular bacterial flagellum reveals mechanism for flagellin incorporation
Authors: Qin, K. / Einenkel, R. / Al-Otaibi, N.S. / Schmidt, J. / Mann, D. / Drobnic, T. / Cohen, E.J. / Rodriguez, N.G. / Harrowell, J. / Shmakova, E. / Beeby, E. / Erhardt, E. / Bergeron, J.R.
History
DepositionSep 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 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
1: Flagellar hook protein FlgE
2: Flagellar hook protein FlgE
3: Flagellar hook protein FlgE
4: Flagellar hook protein FlgE
5: Flagellar hook protein FlgE
6: Flagellar hook protein FlgE
7: Flagellar hook protein FlgE
8: Flagellar hook protein FlgE
9: Flagellar hook protein FlgE
A: Flagellar hook-associated protein 1
B: Flagellar hook-associated protein 1
C: Flagellar hook-associated protein 1
D: Flagellar hook-associated protein 1
E: Flagellar hook-associated protein 1
F: Flagellar hook-associated protein 1
G: Flagellar hook-associated protein 1
H: Flagellar hook-associated protein 1
I: Flagellar hook-associated protein 1
J: Flagellar hook-associated protein 1
K: Flagellar hook-associated protein 1
L: Flagellar hook-associated protein
M: Flagellar hook-associated protein
N: Flagellar hook-associated protein
O: Flagellar hook-associated protein
P: Flagellar hook-associated protein
Q: Flagellar hook-associated protein
R: Flagellar hook-associated protein
S: Flagellar hook-associated protein
T: Flagellar hook-associated protein
U: Flagellar hook-associated protein
V: Flagellar hook-associated protein
a: Flagellin
b: Flagellin
c: Flagellin
d: Flagellin
e: Flagellin
f: Flagellin
g: Flagellin
h: Flagellin
i: Flagellin
j: Flagellin
k: Flagellin
l: Flagellin
m: Flagellin
n: Flagellin
o: Flagellin
w: Flagellar hook protein FlgE
x: Flagellar hook protein FlgE
y: Flagellar hook protein FlgE
z: Flagellar hook protein FlgE


Theoretical massNumber of molelcules
Total (without water)2,350,75950
Polymers2,350,75950
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Flagellar hook protein FlgE


Mass: 42233.152 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: A0A663DET8
#2: Protein
Flagellar hook-associated protein 1 / HAP1


Mass: 59153.781 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: P0A1J6
#3: Protein
Flagellar hook-associated protein / Flagellar hook-filament junction protein FlgL


Mass: 34201.965 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: A0A0W3L1H3
#4: Protein
Flagellin


Mass: 51654.344 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Salmonella enterica (bacteria) / References: UniProt: Q6V2T3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Shorten flagella of Salmonella enterica / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.13 MDa / Experimental value: NO
Source (natural)Organism: Salmonella enterica (bacteria)
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 R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 88 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65561 / Num. of class averages: 1 / Symmetry type: POINT

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