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- PDB-8cye: Cryo-EM asymmetric reconstruction of the EPEC H6 bacterial flagel... -

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Basic information

Entry
Database: PDB / ID: 8cye
TitleCryo-EM asymmetric reconstruction of the EPEC H6 bacterial flagellar filament Normal Waveform
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / Bacterial flagellum / flagellin / bacterial motility / supercoiling
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin, H7-serospecific domain / Flagellin protein / 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 speciesEscherichia coli O127:H6 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKreutzberger, M.A.B. / Chatterjee, S. / Frankel, G. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Cell / Year: 2022
Title: Convergent evolution in the supercoiling of prokaryotic flagellar filaments.
Authors: Mark A B Kreutzberger / Ravi R Sonani / Junfeng Liu / Sharanya Chatterjee / Fengbin Wang / Amanda L Sebastian / Priyanka Biswas / Cheryl Ewing / Weili Zheng / Frédéric Poly / Gad Frankel / ...Authors: Mark A B Kreutzberger / Ravi R Sonani / Junfeng Liu / Sharanya Chatterjee / Fengbin Wang / Amanda L Sebastian / Priyanka Biswas / Cheryl Ewing / Weili Zheng / Frédéric Poly / Gad Frankel / B F Luisi / Chris R Calladine / Mart Krupovic / Birgit E Scharf / Edward H Egelman /
Abstract: The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of ...The supercoiling of bacterial and archaeal flagellar filaments is required for motility. Archaeal flagellar filaments have no homology to their bacterial counterparts and are instead homologs of bacterial type IV pili. How these prokaryotic flagellar filaments, each composed of thousands of copies of identical subunits, can form stable supercoils under torsional stress is a fascinating puzzle for which structural insights have been elusive. Advances in cryoelectron microscopy (cryo-EM) make it now possible to directly visualize the basis for supercoiling, and here, we show the atomic structures of supercoiled bacterial and archaeal flagellar filaments. For the bacterial flagellar filament, we identify 11 distinct protofilament conformations with three broad classes of inter-protomer interface. For the archaeal flagellar filament, 10 protofilaments form a supercoil geometry supported by 10 distinct conformations, with one inter-protomer discontinuity creating a seam inside of the curve. Our results suggest that convergent evolution has yielded stable superhelical geometries that enable microbial locomotion.
History
DepositionMay 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
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Revision 1.3Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,239,52422
Polymers1,239,52422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Flagellin


Mass: 56342.008 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Escherichia coli O127:H6 (bacteria) / References: UniProt: B7USU2
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: Bacterial flagellar filaments / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia coli O127:H6 (bacteria) / Strain: O127:H6
Buffer solutionpH: 7.4
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19rc4_4035: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 46895 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00344328
ELECTRON MICROSCOPYf_angle_d0.60959988
ELECTRON MICROSCOPYf_dihedral_angle_d5.0236180
ELECTRON MICROSCOPYf_chiral_restr0.0367370
ELECTRON MICROSCOPYf_plane_restr0.0038138

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