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- EMDB-10362: Cryo-EM structure of the wild-type flagellar filament of the Firm... -

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Basic information

Entry
Database: EMDB / ID: EMD-10362
TitleCryo-EM structure of the wild-type flagellar filament of the Firmicute Kurthia
Map data
Sample
  • Complex: Flagellar Filament
    • Protein or peptide: Flagellin
Function / homologybacterial-type flagellum filament / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / bacterial-type flagellum-dependent cell motility / structural molecule activity / extracellular region / Flagellin
Function and homology information
Biological speciesKurthia sp. 11kri321 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBlum TB / Abrahams JP
Funding support Switzerland, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_17002 Switzerland
Swiss National Science Foundation31003A_152972 Switzerland
Swiss National Science Foundation200021_165669 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, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseOct 30, 2019-
UpdateOct 30, 2019-
Current statusOct 30, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t17
  • Surface level: 0.0244
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6t17
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10362.png

Downloads & links

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Map

FileDownload / File: emd_10362.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.058 Å
Density
Contour LevelBy AUTHOR: 0.0244 / Movie #1: 0.0244
Minimum - Maximum-0.023902241 - 0.061274417
Average (Standard dev.)0.00032706262 (±0.005256356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.848 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0581.0581.058
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z270.848270.848270.848
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ307236
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0240.0610.000

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Supplemental data

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Sample components

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Entire : Flagellar Filament

EntireName: Flagellar Filament
Components
  • Complex: Flagellar Filament
    • Protein or peptide: Flagellin

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Supramolecule #1: Flagellar Filament

SupramoleculeName: Flagellar Filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Kurthia sp. 11kri321 (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 44 / Enantiomer: LEVO
Source (natural)Organism: Kurthia sp. 11kri321 (bacteria)
Molecular weightTheoretical: 29.530055 KDa
Recombinant expressionOrganism: Kurthia sp. 11kri321 (bacteria)
SequenceString: MRIQHNIAAL NTHRNLAANN AAASKNLEKL SSGFKINRAG DDAAGLAISE KMRGQISGLN MASKNSSDAI SLIQTAEGGL NETHAILQR MRELAVQSRN DTNDEATNDR SNLNDELKQL QEEITRISSQ MEFNNKKLLD GSQSTNGLTF QIGANAGQTI T MKISTMSA ...String:
MRIQHNIAAL NTHRNLAANN AAASKNLEKL SSGFKINRAG DDAAGLAISE KMRGQISGLN MASKNSSDAI SLIQTAEGGL NETHAILQR MRELAVQSRN DTNDEATNDR SNLNDELKQL QEEITRISSQ MEFNNKKLLD GSQSTNGLTF QIGANAGQTI T MKISTMSA TKLGVDAAKA SISKGTAASK AIKSIDDAIN TVSKTRSALG AVQNRLEHTI NNLGTSAENL TAAESRIRDT DM AAEMMAF TKNNILTQAA QSMLAQANQQ PQGVLQLLQ

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 86.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Sub-tomogram average
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.83 Å
Applied symmetry - Helical parameters - Δ&Phi: 65.45 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9270
FSC plot (resolution estimation)

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