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- EMDB-72942: Flagella filament structure in H. pylori composed of flagellin FlaA -

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Basic information

Entry
Database: EMDB / ID: EMD-72942
TitleFlagella filament structure in H. pylori composed of flagellin FlaA
Map dataEM_MAP_FlaA
Sample
  • Organelle or cellular component: Flagella filament
    • Protein or peptide: Flagellin
  • Ligand: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
Keywordsflagellin / STRUCTURAL PROTEIN
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
Biological speciesHelicobacter pylori (bacteria) / Helicobacter pylori B128 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKumar R / Yu H / Tachiyama S / Liu J
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72942.png

Downloads & links

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Map

FileDownload / File: emd_72942.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM_MAP_FlaA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 427.2 Å		1.07 Å/pix.
x 400 pix.
= 427.2 Å		1.07 Å/pix.
x 400 pix.
= 427.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.111
Minimum - Maximum-0.3628719 - 0.7765726
Average (Standard dev.)0.007073129 (±0.040608376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 427.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map FlaA B

Fileemd_72942_half_map_1.map
AnnotationHalf map FlaA_B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map FlaA A

Fileemd_72942_half_map_2.map
AnnotationHalf map FlaA_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Flagella filament

EntireName: Flagella filament
Components
  • Organelle or cellular component: Flagella filament
    • Protein or peptide: Flagellin
  • Ligand: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid

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Supramolecule #1: Flagella filament

SupramoleculeName: Flagella filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Flagellin FlaA glycosylated with pseudaminic acid
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: B120

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori B128 (bacteria)
Molecular weightTheoretical: 53.067848 KDa
SequenceString: AFQVNTNINA MNAHVQSALT QNALKTSLER LSSGLRINKA ADDASGMTVA DSLRSQASSL GQAIANTNDG MGIIQVADKA MDEQLKILD TVKVKATQAA QDGQTTESRK AIQSDIVRLI QGLDNIGNTT TYNGQALLSG QFTNKEFQVG AYSNQSIKAS I GSTTSDKI ...String:
AFQVNTNINA MNAHVQSALT QNALKTSLER LSSGLRINKA ADDASGMTVA DSLRSQASSL GQAIANTNDG MGIIQVADKA MDEQLKILD TVKVKATQAA QDGQTTESRK AIQSDIVRLI QGLDNIGNTT TYNGQALLSG QFTNKEFQVG AYSNQSIKAS I GSTTSDKI GQVRIATGAL ITASGDISLT FKQVDGVNDV TLESVKVSSS AGTGIGVLAE VINKNSNRTG VKAYASVITT SD VAVQSGS LSNLTLNGIH LGNIADIKKN DSDGRLVAAI NAVTSETGVE AYTDQKGRLN LRSIDGRGIE IKTDSVGNGP SAL TMVNGG QDLTKGSTNY GRLSLTRLDA KSINVVSASD SQHLGFTAIG FGESQVAETT VNLRDVTGNF NANVKSASGA NYNA VIASG NQSLGSGVTT LRGAMVVIDI AESAMKMLDK VRSDLGSVQN QMISTVNNIS ITQVNVKAAE SQIRDVDFAE ESANF NKNN ILAQSGSYAM SQANTVQQNI LRLL

UniProtKB: Flagellin

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Macromolecule #2: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulop...

MacromoleculeName: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
type: ligand / ID: 2 / Number of copies: 231 / Formula: P8E
Molecular weightTheoretical: 250.249 Da
Chemical component information

ChemComp-P8E:
5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 98 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 228410
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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