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- PDB-6x80: Structure of the Campylobacter jejuni G508A Flagellar Filament -

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Basic information

Entry
Database: PDB / ID: 6x80
TitleStructure of the Campylobacter jejuni G508A Flagellar Filament
ComponentsFlagellin A
KeywordsSTRUCTURAL PROTEIN / Helical Symmetry / Bacterial Flagellar Filament
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
Chem-P8E / Flagellin A
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKreutzberger, M.A.B. / Wang, F. / Egelman, E.H.
Funding support United States, 2items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type
Revision 2.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Apr 27, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.3May 15, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Flagellin A
B: Flagellin A
C: Flagellin A
D: Flagellin A
E: Flagellin A
F: Flagellin A
G: Flagellin A
H: Flagellin A
I: Flagellin A
J: Flagellin A
K: Flagellin A
L: Flagellin A
M: Flagellin A
N: Flagellin A
O: Flagellin A
P: Flagellin A
Q: Flagellin A
R: Flagellin A
S: Flagellin A
T: Flagellin A
U: Flagellin A
V: Flagellin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,404,590396
Polymers1,310,99722
Non-polymers93,593374
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellin A


Mass: 59590.762 Da / Num. of mol.: 22 / Mutation: G508A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: flaA / Production host: Campylobacter jejuni (Campylobacter) / References: UniProt: P22251
#2: Sugar...
ChemComp-P8E / 5,7-diamino-3,5,7,9-tetradeoxy-L-glycero-alpha-L-manno-non-2-ulopyranosonic acid


Type: L-saccharide, alpha linking / Mass: 250.249 Da / Num. of mol.: 374 / Source method: obtained synthetically / Formula: C9H18N2O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Bacterial Flagellar Filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: MULTIPLE SOURCES
Source (natural)Organism: Campylobacter jejuni (Campylobacter)
Source (recombinant)Organism: Campylobacter jejuni (Campylobacter)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameCategory
13SPIDER3D reconstruction
14RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.32 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 116959 / Details: MODEL:MAP FSC using a threshold of 0.5 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006200565
ELECTRON MICROSCOPYf_angle_d0.594271575
ELECTRON MICROSCOPYf_dihedral_angle_d2.77114075
ELECTRON MICROSCOPYf_chiral_restr0.04134380
ELECTRON MICROSCOPYf_plane_restr0.00234290

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