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- PDB-6t17: Cryo-EM structure of the wild-type flagellar filament of the Firm... -

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Basic information

Entry
Database: PDB / ID: 6t17
TitleCryo-EM structure of the wild-type flagellar filament of the Firmicute Kurthia
ComponentsFlagellin
KeywordsPROTEIN FIBRIL / Gram-Positive Bacteria Flagella / Helical / Wild-Type
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
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 speciesKurthia sp. 11kri321 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBlum, T.B. / Abrahams, J.P.
Funding support Switzerland, 4items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_17002 Switzerland
Swiss National Science Foundation200021_165669 Switzerland
Swiss National Science Foundation31003A_152972 Switzerland
Swiss National Science Foundation31003A_179297 Switzerland
CitationJournal: Sci Rep / Year: 2019
Title: The wild-type flagellar filament of the Firmicute Kurthia at 2.8 Å resolution in vivo.
Authors: Thorsten B Blum / Sevasti Filippidou / Mathilda Fatton / Pilar Junier / Jan Pieter Abrahams /
Abstract: Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the ...Bacteria swim and swarm by rotating the micrometers long, helical filaments of their flagella. They change direction by reversing their flagellar rotation, which switches the handedness of the filament's supercoil. So far, all studied functional filaments are composed of a mixture of L- and R-state flagellin monomers. Here we show in a study of the wild type Firmicute Kurthia sp., that curved, functional filaments can adopt a conformation in vivo that is closely related to a uniform, all-L-state. This sheds additional light on transitions of the flagellar supercoil and uniquely reveals the atomic structure of a wild-type flagellar filament in vivo, including six residues showing clearly densities of O-linked glycosylation.
History
DepositionOct 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)1,299,32244
Polymers1,299,32244
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Sub-tomogram averaging
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area331430 Å2
ΔGint-1322 kcal/mol
Surface area409390 Å2
MethodPISA

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Components

#1: Protein ...
Flagellin


Mass: 29530.055 Da / Num. of mol.: 44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kurthia sp. 11kri321 (bacteria) / Gene: ASO14_2420 / Production host: Kurthia sp. 11kri321 (bacteria) / References: UniProt: A0A0X9VHV9

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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: Flagellar Filament / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Kurthia sp. 11kri321 (bacteria)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen 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: 86 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 65.45 ° / Axial rise/subunit: 4.83 Å / Axial symmetry: C1
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9270 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: HELICAL

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