9M68 | pdb_00009m68

the flagellar filament cap FliD in complex with FlgL


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9M68

This is version 1.1 of the entry. See complete history

Literature

Ultraweak interactions drive cap-mediated positioning and elongation of the bacterial flagellar filament.

Chen, L.Cheng, X.Zhang, F.Dong, X.Wang, X.Jiang, W.Ma, L.Xing, Q.

(2025) Nat Commun 17: 1127-1127

  • DOI: https://doi.org/10.1038/s41467-025-67887-y
  • Primary Citation Related Structures: 
    9M67, 9M68, 9M6H, 9M6I

  • PubMed Abstract: 

    The bacterial flagellum, essential for motility and pathogenesis, requires the filament cap (FliD) to polymerize flagellin (FliC). However, the mechanisms governing the transition from the hook junction to the filament elongation remain elusive, obscured by stoichiometric mismatches and barely detectable interactions. To resolve this, we deploy solution NMR to characterize ultra-weak interactions, quantify affinities (K D  ≈ 0.1 mM for junction protein FlgL; 1.65 mM for FliC). These data enable rational complex stabilization for cryo-EM structure determination of Salmonella FliD pentamers complexed with FlgL or FliC, revealing that both substrates engage an identical conserved surface in a 5:5 stoichiometry. Integrating these structures into native flagellar tip densities reveal a 5:11 FliD:FlgL/FliC architecture, where six additional subunits barely detected by NMR dock at secondary sites. Mutations that disrupt or enhance these interfaces impair motility and filament integrity, while disulfide-locked FliD pentamers confirm that cap rigidity is crucial for elongation. These findings support a rotary cap mechanism where ultra-weak binding and structural fidelity of the cap ensure efficient flagellin polymerization. Our study resolves the long-standing paradox of stoichiometric mismatch in flagellar filament biogenesis, providing a blueprint for the assembly of dynamic macromolecular machines.


  • Organizational Affiliation
    • State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 339.01 kDa 
  • Atom Count: 23,750 
  • Modeled Residue Count: 3,190 
  • Deposited Residue Count: 3,190 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Flagellar hook-associated protein 2A,
C [auth B],
E [auth D],
G,
I
415Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: fliDflaVflbCSTM1960
UniProt
Find proteins for P16328 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P16328 
Go to UniProtKB:  P16328
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16328
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Flagellar hook-associated protein 3B [auth F],
D [auth C],
F [auth E],
H,
J
223Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: flgLflaTflaUSTM1184
UniProt
Find proteins for P16326 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P16326 
Go to UniProtKB:  P16326
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16326
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONcryoSPARC4.01

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371277

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references