[English] 日本語
Yorodumi
- EMDB-72948: Structure of flagellin FlaB filament in H. pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72948
TitleStructure of flagellin FlaB filament in H. pylori
Map dataFlagellin FlaB filament in H. pylori
Sample
  • Cell: Flagellar filament composed of flagellin FlaB
    • Protein or peptide: Flagellin
  • Ligand: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
KeywordsFlagella / Flagellin / Filament / 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: 3.22 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

-
Structure visualization

Supplemental images

emd_72948.png

Downloads & links

-
Map

FileDownload / File: emd_72948.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFlagellin FlaB filament in H. pylori
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 Å		1.07 Å/pix.
x 448 pix.
= 478.464 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: 0.052
Minimum - Maximum-0.14710149 - 0.2815027
Average (Standard dev.)0.0041870046 (±0.018501863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 478.464 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: FlaB Half map B

Fileemd_72948_half_map_1.map
AnnotationFlaB Half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: FlaB Half map A

Fileemd_72948_half_map_2.map
AnnotationFlaB Half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Flagellar filament composed of flagellin FlaB

EntireName: Flagellar filament composed of flagellin FlaB
Components
  • Cell: Flagellar filament composed of flagellin FlaB
    • Protein or peptide: Flagellin
  • Ligand: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid

-
Supramolecule #1: Flagellar filament composed of flagellin FlaB

SupramoleculeName: Flagellar filament composed of flagellin FlaB / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Helicobacter pylori (bacteria)

-
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: 53.88966 KDa
SequenceString: SFRINTNIAA LTSHAVGVQN NRDLSSSLEK LSSGLRINKA ADDSSGMAIA DSLRSQSANL GQAIRNANDA IGMVQTADKA MDEQIKILD TIKTKAVQAA QDGQTLESRR ALQSDIQRLL EELDNIANTT SFNGQQMLSG SFSNKEFQIG AYSNTTVKAS I GSTSSDKI ...String:
SFRINTNIAA LTSHAVGVQN NRDLSSSLEK LSSGLRINKA ADDSSGMAIA DSLRSQSANL GQAIRNANDA IGMVQTADKA MDEQIKILD TIKTKAVQAA QDGQTLESRR ALQSDIQRLL EELDNIANTT SFNGQQMLSG SFSNKEFQIG AYSNTTVKAS I GSTSSDKI GHVRMETSSF SGEGMLASAA AQNLTEVGLN FKQVNGVNDY KIETVRISTS AGTGIGALSE IINRFSNTLG VR ASYNVMA TGGTPVQSGT VRELTINGVE IGTVNDVHKN DADGRLTNAI NSVKDRTGVE ASLDIQGRIN LHSIDGRAIS VHA ASASGQ VFGGGNFAGI SGTQHAVIGR LTLTRTDARD IIVSGVNFSH VGFHSAQGVA EYTVNLRAVR GIFDANVASA AGAN ANGAQ AETNSQGIGA GVTSLKGAMI VMDMADSART QLDKIRSDMG SVQMELVTTI NNISVTQVNV KAAESQIRDV DFAEE SANF SKYNILAQSG SFAMAQANAV QQNVLRLLQ

UniProtKB: Flagellin

-
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: 297 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 60029
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more