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- PDB-8cwm: Cryo-EM structure of the supercoiled S. islandicus REY15A archaea... -

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Basic information

Entry
Database: PDB / ID: 8cwm
TitleCryo-EM structure of the supercoiled S. islandicus REY15A archaeal flagellar filament
ComponentsFlagellin
KeywordsSTRUCTURAL PROTEIN / Archaea / Motility / supercoiling
Function / homologyarchaeal-type flagellum / Flagellin/pilin, N-terminal / Flagellin, archaea / Archaebacterial flagellin / archaeal or bacterial-type flagellum-dependent cell motility / membrane => GO:0016020 / structural molecule activity / Flagellin
Function and homology information
Biological speciesSulfolobus islandicus REY15A (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKreutzberger, M.A.B. / Liu, J. / Krupovic, M. / 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 19, 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _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

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Assembly

Deposited unit
0: Flagellin
1: Flagellin
2: Flagellin
3: Flagellin
4: Flagellin
5: Flagellin
6: Flagellin
7: Flagellin
A: 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
Z: Flagellin
a: 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
z: Flagellin


Theoretical massNumber of molelcules
Total (without water)1,988,01060
Polymers1,988,01060
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: 33133.500 Da / Num. of mol.: 60 / Source method: isolated from a natural source
Source: (natural) Sulfolobus islandicus REY15A (acidophilic)
Strain: REY15A / References: UniProt: F0NG73

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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: Archaeal flagellar filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sulfolobus islandicus (acidophilic) / Strain: REY15A
Buffer solutionpH: 3
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: 1000 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: 3.4 Å / Resolution method: FSC 0.33 CUT-OFF / Num. of particles: 51914 / Symmetry type: POINT

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