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- PDB-9yh1: Structure of flagellin FlaB filament in H. pylori -

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Basic information

Entry
Database: PDB / ID: 9yh1
TitleStructure of flagellin FlaB filament in H. pylori
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / Flagella / Flagellin / Filament
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
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
Chem-P8E / Flagellin
Similarity search - Component
Biological speciesHelicobacter pylori B128 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsKumar, R. / Yu, H. / Tachiyama, S. / Liu, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1S10 OD023603-01A1 United States
CitationJournal: PNAS Nexus / Year: 2026
Title: Assembly and glycosylation of sheathed flagella.
Authors: Rajeev Kumar / Shoichi Tachiyama / Huaxin Yu / Samira Heydari / Jiaqi Guo / Jack M Botting / Wangbiao Guo / Timothy R Hoover / Jun Liu /
Abstract: The bacterial flagellum is a complex nanomachine essential for motility, colonization, and invasion in diverse species. has evolved elaborate sheathed flagella that enable migration through the ...The bacterial flagellum is a complex nanomachine essential for motility, colonization, and invasion in diverse species. has evolved elaborate sheathed flagella that enable migration through the highly viscous gastric mucus layer to reach its colonization niche on the gastric epithelium, yet the molecular basis for these unique adaptations has remained elusive. Here, we use in situ single-particle cryo-electron microscopy to determine near-atomic structures of the flagellar filament within the membranous sheath of . The major flagellin FlaA constitutes the bulk of the filament, whereas the minor flagellin FlaB contributes critically to the hook-proximal region. Both FlaA and FlaB form a conserved core surrounded by variable surface-exposed domains. Our structures further reveal that pseudaminic acid glycans decorate these domains, where they mediate inter- and intra-subunit contacts that stabilize the filament and confer a negatively charged surface. Together, these findings support a model in which the filament rotates independently of the membranous sheath to drive motility and provide a molecular framework for understanding how the sheathed flagellum enables colonization and persistence within the gastric niche.
History
DepositionSep 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data 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
A1: Flagellin
A2: Flagellin
A3: Flagellin
A4: Flagellin
A5: Flagellin
A6: Flagellin
A7: Flagellin
A8: Flagellin
A9: Flagellin
AA: Flagellin
AB: Flagellin
AC: Flagellin
AD: Flagellin
AE: Flagellin
AF: Flagellin
AG: Flagellin
AH: Flagellin
AI: Flagellin
AJ: Flagellin
AK: Flagellin
AL: Flagellin
AM: Flagellin
AN: Flagellin
AO: Flagellin
AP: Flagellin
AQ: Flagellin
AR: Flagellin
AS: Flagellin
AT: Flagellin
AU: Flagellin
AV: Flagellin
AW: Flagellin
AX: Flagellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,852,683330
Polymers1,778,35933
Non-polymers74,324297
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


Mass: 53889.660 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Source: (natural) Helicobacter pylori B128 (bacteria) / References: UniProt: Q6VYQ1
#2: Sugar...
ChemComp-P8E / 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid / Pse5Ac7Ac


Type: D-saccharide, beta linking / Mass: 250.249 Da / Num. of mol.: 297 / Source method: obtained synthetically / Formula: C9H18N2O6
Has ligand of interestN
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: Flagellar filament composed of flagellin FlaB / Type: CELL / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Helicobacter pylori (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60029 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 110.5 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027130152
ELECTRON MICROSCOPYf_angle_d0.4522176121
ELECTRON MICROSCOPYf_chiral_restr0.035621648
ELECTRON MICROSCOPYf_plane_restr0.001922935
ELECTRON MICROSCOPYf_dihedral_angle_d7.41720055

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