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- PDB-8cxm: Cryo-EM structure of the supercoiled E. coli K12 flagellar filame... -

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Basic information

Entry
Database: PDB / ID: 8cxm
TitleCryo-EM structure of the supercoiled E. coli K12 flagellar filament core, Normal waveform
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / Bacterial motility / flagellar filament / flagellin
Function / homology
Function and homology information


Toll Like Receptor 5 (TLR5) Cascade / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin D3 / : / Flagellin D3 domain / Flagellin, barrel domain / 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 K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsSonani, R.R. / Kreutzberger, M.A.B. / Sebastian, A.L. / Scharf, B. / 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 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Z: Flagellin
B: Flagellin
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin
T: Flagellin
U: Flagellin
V: Flagellin
W: Flagellin
X: Flagellin
Y: Flagellin
a: Flagellin
b: Flagellin
c: Flagellin
d: Flagellin
e: Flagellin
2: Flagellin
f: Flagellin
g: Flagellin
h: Flagellin
i: Flagellin
j: Flagellin
k: Flagellin
A: Flagellin
l: Flagellin
m: Flagellin
n: Flagellin
o: Flagellin
p: Flagellin
q: Flagellin
r: Flagellin
s: Flagellin
t: Flagellin
u: Flagellin
v: Flagellin
w: Flagellin
x: Flagellin
y: Flagellin
z: Flagellin
0: Flagellin
1: Flagellin


Theoretical massNumber of molelcules
Total (without water)2,823,18255
Polymers2,823,18255
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: 51330.582 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Variant: MG1655 / Strain: K12 / References: UniProt: P04949

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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: E. coli K12 flagellar filament core / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: MG1655
Buffer solutionpH: 7.2
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: 2200 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49279 / Symmetry type: POINT

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