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- PDB-9m68: the flagellar filament cap FliD in complex with FlgL -

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Basic information

Entry
Database: PDB / ID: 9m68
Titlethe flagellar filament cap FliD in complex with FlgL
Components
  • Flagellar hook-associated protein 2
  • Flagellar hook-associated protein 3
KeywordsSTRUCTURAL PROTEIN / Complex
Function / homology
Function and homology information


bacterial-type flagellum filament cap / bacterial-type flagellum hook / bacterial-type flagellum-dependent cell motility / cell adhesion / structural molecule activity / extracellular region
Similarity search - Function
Flagellar hook-associated protein 3 / Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellar hook-associated protein 2 / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Flagellar hook-associated protein 3 / Flagellar hook-associated protein 2
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsXing, Q. / Cheng, X.Q. / Jiang, W.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371277 China
CitationJournal: To Be Published
Title: Structural insights into the initiation of bacterial flagellar filament elongation
Authors: Chen, L.X. / Dong, X. / Zhang, F.F. / Cheng, X.Q. / Wang, X. / Jiang, W.X. / Ma, L.X. / Xing, Q.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 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: Flagellar hook-associated protein 2
F: Flagellar hook-associated protein 3
B: Flagellar hook-associated protein 2
C: Flagellar hook-associated protein 3
D: Flagellar hook-associated protein 2
E: Flagellar hook-associated protein 3
G: Flagellar hook-associated protein 2
H: Flagellar hook-associated protein 3
I: Flagellar hook-associated protein 2
J: Flagellar hook-associated protein 3


Theoretical massNumber of molelcules
Total (without water)339,00610
Polymers339,00610
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-associated protein 2 / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 44168.105 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Salmonella enterica subsp. enterica serovar Typhimurium' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id P16328.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliD, flaV, flbC, STM1960 / Production host: Escherichia coli (E. coli) / References: UniProt: P16328
#2: Protein
Flagellar hook-associated protein 3 / HAP3 / Hook-filament junction protein


Mass: 23633.057 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Salmonella enterica subsp. enterica serovar Typhimurium' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id P16326.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: flgL, flaT, flaU, STM1184 / Production host: Escherichia coli (E. coli) / References: UniProt: P16326
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: FliD with FlgL / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.01particle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC4.013D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 453039 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00423925
ELECTRON MICROSCOPYf_angle_d0.5232395
ELECTRON MICROSCOPYf_dihedral_angle_d4.3363320
ELECTRON MICROSCOPYf_chiral_restr0.0384020
ELECTRON MICROSCOPYf_plane_restr0.0044205

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