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- EMDB-22088: Structure of the Campylobacter jejuni G508A Flagellar Filament -

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Basic information

Entry
Database: EMDB / ID: EMD-22088
TitleStructure of the Campylobacter jejuni G508A Flagellar Filament
Map data
Sample
  • Organelle or cellular component: Bacterial Flagellar Filament
    • Protein or peptide: Flagellin A
  • Ligand: 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid
KeywordsHelical Symmetry / Bacterial Flagellar Filament / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial-type flagellum filament / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region
Similarity search - Function
Flagellin hook, IN motif / Flagellin hook IN motif / Flagellin, C-terminal domain, subdomain 2 / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni (Campylobacter)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKreutzberger MAB / Wang F / Egelman EH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM080186 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Atomic structure of the flagellar filament reveals how ε Proteobacteria escaped Toll-like receptor 5 surveillance.
Authors: Mark A B Kreutzberger / Cheryl Ewing / Frederic Poly / Fengbin Wang / Edward H Egelman /
Abstract: Vertebrates, from zebra fish to humans, have an innate immune recognition of many bacterial flagellins. This involves a conserved eight-amino acid epitope in flagellin recognized by the Toll-like ...Vertebrates, from zebra fish to humans, have an innate immune recognition of many bacterial flagellins. This involves a conserved eight-amino acid epitope in flagellin recognized by the Toll-like receptor 5 (TLR5). Several important human pathogens, such as and , have escaped TLR5 activation by mutations in this epitope. When such mutations were introduced into flagellin, motility was abolished. It was previously argued, using very low-resolution cryoelectron microscopy (cryo-EM), that accommodated these mutations by forming filaments with 7 protofilaments, rather than the 11 found in other bacteria. We have now determined the atomic structure of the G508A flagellar filament from a 3.5-Å-resolution cryo-EM reconstruction, and show that it has 11 protofilaments. The residues in the TLR5 epitope have reduced contacts with the adjacent subunit compared to other bacterial flagellar filament structures. The weakening of the subunit-subunit interface introduced by the mutations in the TLR5 epitope is compensated for by extensive interactions between the outer domains of the flagellin subunits. In other bacteria, these outer domains can be nearly absent or removed without affecting motility. Furthermore, we provide evidence for the stabilization of these outer domain interactions through glycosylation of key residues. These results explain the essential role of glycosylation in motility, and show how the outer domains have evolved to play a role not previously found in other bacteria.
History
DepositionJun 1, 2020-
Header (metadata) releaseJul 8, 2020-
Map releaseJul 8, 2020-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x80
  • Surface level: 0.0054
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x80
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22088.png

Downloads & links

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Map

FileDownload / File: emd_22088.map.gz / Format: CCP4 / Size: 236.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.0054 / Movie #1: 0.0054
Minimum - Maximum-0.0080477325 - 0.019455412
Average (Standard dev.)0.00032223167 (±0.0016402273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384420
Spacing384384420
CellA: 414.72003 Å / B: 414.72003 Å / C: 453.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z384384420
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720453.600
α/β/γ90.00090.00090.000
start NX/NY/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384420
D min/max/mean-0.0080.0190.000

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Supplemental data

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Sample components

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Entire : Bacterial Flagellar Filament

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

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Supramolecule #1: Bacterial Flagellar Filament

SupramoleculeName: Bacterial Flagellar Filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Campylobacter jejuni (Campylobacter)

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Macromolecule #1: Flagellin A

MacromoleculeName: Flagellin A / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Molecular weightTheoretical: 59.590762 KDa
Recombinant expressionOrganism: Campylobacter jejuni (Campylobacter)
SequenceString: MGFRINTNVA ALNAKANSDL NAKSLDASLS RLSSGLRINS AADDASGMAI ADSLRSQANT LGQAISNGND ALGILQTADK AMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS GNFTNQEFQI GASSNQTVKA T IGATQSSK ...String:
MGFRINTNVA ALNAKANSDL NAKSLDASLS RLSSGLRINS AADDASGMAI ADSLRSQANT LGQAISNGND ALGILQTADK AMDEQLKIL DTIKTKATQA AQDGQSLKTR TMLQADINKL MEELDNIANT TSFNGKQLLS GNFTNQEFQI GASSNQTVKA T IGATQSSK IGVTRFETGA QSFTSGVVGL TIKNYNGIED FKFDNVVIST SVGTGLGALA EEINKSADKT GVRATYDVKT TG VYAIKEG TTSQDFAING VTIGKIEYKD GDGNGSLISA INAVKDTTGV QASKDENGKL VLTSADGRGI KITGDIGVGS GIL ANQKEN YGRLSLVKND GRDINISGTN LSAIGMGTTD MISQSSVSLR ESKGQISATN ADAMGFNSYK GGGKFVFTQN VSSI SAFMS AQGSGFSRGS GFSVGSGKNL SVGLSQGIQI ISSAASMSNT YVVSAGSGFS SGSGNSQFAA LKTTAANTTD ETAGV TTLK GAMAVMDIAE TAITNLDQIR ADIASIQNQV TSTINNITVT QVNVKAAESQ IRDVDFASES ANYSKANILA QSGSYA MAQ ANSSQQNVLR LLQ

UniProtKB: Flagellin A

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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: 374 / 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
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.32 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software: (Name: SPIDER, RELION) / Details: MODEL:MAP FSC using a threshold of 0.5 / Number images used: 116959
Startup modelType of model: OTHER
Details: averaged cylinder using all segments, with random azimuthal angles
Final angle assignmentType: NOT APPLICABLE

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