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- PDB-9m67: the flagellar filament cap FliD in complex with FliC -

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Basic information

Entry
Database: PDB / ID: 9m67
Titlethe flagellar filament cap FliD in complex with FliC
ComponentsFlagellin,Flagellar hook-associated protein 2
KeywordsSTRUCTURAL PROTEIN / Complex
Function / homology
Function and homology information


TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / bacterial-type flagellum filament cap / bacterial-type flagellum hook / The IPAF inflammasome / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / cell adhesion / receptor ligand activity ...TLR5 cascade / MyD88 cascade initiated on plasma membrane / NFkB and MAPK activation mediated by TRAF6 / bacterial-type flagellum filament cap / bacterial-type flagellum hook / The IPAF inflammasome / bacterial-type flagellum / bacterial-type flagellum-dependent cell motility / cell adhesion / receptor ligand activity / structural molecule activity / extracellular space / extracellular region
Similarity search - Function
Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellin D3 / Flagellar hook-associated protein 2 / : / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin D3 domain / Flagellin, barrel domain / Flagellin hook, IN motif ...Flagellar hook-associated protein 2, N-terminal / Flagellar hook-associated protein 2, C-terminal / Flagellin D3 / Flagellar hook-associated protein 2 / : / Flagellar hook-associated protein 2 N-terminus / Flagellar hook-associated protein 2 C-terminus / Flagellin D3 domain / Flagellin, barrel domain / Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / 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
Flagellin / 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: 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

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Assembly

Deposited unit
A: Flagellin,Flagellar hook-associated protein 2
B: Flagellin,Flagellar hook-associated protein 2
C: Flagellin,Flagellar hook-associated protein 2
D: Flagellin,Flagellar hook-associated protein 2
E: Flagellin,Flagellar hook-associated protein 2
F: Flagellin,Flagellar hook-associated protein 2
G: Flagellin,Flagellar hook-associated protein 2
H: Flagellin,Flagellar hook-associated protein 2
I: Flagellin,Flagellar hook-associated protein 2
J: Flagellin,Flagellar hook-associated protein 2


Theoretical massNumber of molelcules
Total (without water)1,048,13410
Polymers1,048,13410
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
Flagellin,Flagellar hook-associated protein 2 / Phase 1-I flagellin / HAP2 / Filament cap protein / Flagellar cap protein


Mass: 104813.438 Da / Num. of mol.: 10
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 P06179/P16328.
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: fliC, flaF, hag, STM1959, fliD, flaV, flbC, STM1960 / Production host: Escherichia coli (E. coli) / References: UniProt: P06179, UniProt: P16328
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 flagellar filament cap FliD in complex with FliC / 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
SpecimenConc.: 4 mg/ml / Embedding 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 softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 903918 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00330855
ELECTRON MICROSCOPYf_angle_d0.48341825
ELECTRON MICROSCOPYf_dihedral_angle_d4.4634330
ELECTRON MICROSCOPYf_chiral_restr0.0395190
ELECTRON MICROSCOPYf_plane_restr0.0045460

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