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- EMDB-25382: Cryo-EM structure of the Achromobacter flagellar filament -

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Basic information

Entry
Database: EMDB / ID: EMD-25382
TitleCryo-EM structure of the Achromobacter flagellar filament
Map data
Sample
  • Complex: Bacterial flagellar filament
    • Protein or peptide: Flagellin
KeywordsBacterial flagella / motility / soil / STRUCTURAL PROTEIN
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 speciesAchromobacter sp. (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKreutzberger MA / Wang F / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: Nat Commun / Year: 2022
Title: Flagellin outer domain dimerization modulates motility in pathogenic and soil bacteria from viscous environments.
Authors: Mark A B Kreutzberger / Richard C Sobe / Amber B Sauder / Sharanya Chatterjee / Alejandro Peña / Fengbin Wang / Jorge A Giron / Volker Kiessling / Tiago R D Costa / Vincent P Conticello / ...Authors: Mark A B Kreutzberger / Richard C Sobe / Amber B Sauder / Sharanya Chatterjee / Alejandro Peña / Fengbin Wang / Jorge A Giron / Volker Kiessling / Tiago R D Costa / Vincent P Conticello / Gad Frankel / Melissa M Kendall / Birgit E Scharf / Edward H Egelman /
Abstract: Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in ...Flagellar filaments function as the propellers of the bacterial flagellum and their supercoiling is key to motility. The outer domains on the surface of the filament are non-critical for motility in many bacteria and their structures and functions are not conserved. Here, we show the atomic cryo-electron microscopy structures for flagellar filaments from enterohemorrhagic Escherichia coli O157:H7, enteropathogenic E. coli O127:H6, Achromobacter, and Sinorhizobium meliloti, where the outer domains dimerize or tetramerize to form either a sheath or a screw-like surface. These dimers are formed by 180° rotations of half of the outer domains. The outer domain sheath (ODS) plays a role in bacterial motility by stabilizing an intermediate waveform and prolonging the tumbling of E. coli cells. Bacteria with these ODS and screw-like flagellar filaments are commonly found in soil and human intestinal environments of relatively high viscosity suggesting a role for the dimerization in these environments.
History
DepositionNov 5, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0214
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0214
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sqd
  • Surface level: 0.0214
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7sqd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25382.png

Downloads & links

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Map

FileDownload / File: emd_25382.map.gz / Format: CCP4 / Size: 253.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 450 pix.
= 477. Å		1.06 Å/pix.
x 384 pix.
= 407.04 Å		1.06 Å/pix.
x 384 pix.
= 407.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0214 / Movie #1: 0.0214
Minimum - Maximum-0.03030386 - 0.077274315
Average (Standard dev.)0.0013252039 (±0.006649985)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384450
Spacing384384450
CellA: 407.03998 Å / B: 407.03998 Å / C: 476.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z384384450
origin x/y/z0.0000.0000.000
length x/y/z407.040407.040477.000
α/β/γ90.00090.00090.000
start NX/NY/NZ138136120
NX/NY/NZ121111179
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384450
D min/max/mean-0.0300.0770.001

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Supplemental data

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Sample components

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Entire : Bacterial flagellar filament

EntireName: Bacterial flagellar filament
Components
  • Complex: Bacterial flagellar filament
    • Protein or peptide: Flagellin

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Supramolecule #1: Bacterial flagellar filament

SupramoleculeName: Bacterial flagellar filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Achromobacter sp. (bacteria)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 48 / Enantiomer: LEVO
Source (natural)Organism: Achromobacter sp. (bacteria)
Molecular weightTheoretical: 57.454473 KDa
Recombinant expressionOrganism: Achromobacter sp. (bacteria)
SequenceString: MAAVINTNYL SLVAQNNLNK SQSSLGTAIE RLSSGLRINS AKDDAAGMAI ANRFTANVRG LTQAARNAND GISLAQTTEG AASEVNTHL QRIRELTVQA SNGSYSQEQL DSVQGEINQR LADIDRISEQ TDFNGVKVLS DSAKPLTLQV GANDGETITL N LSEISVKT ...String:
MAAVINTNYL SLVAQNNLNK SQSSLGTAIE RLSSGLRINS AKDDAAGMAI ANRFTANVRG LTQAARNAND GISLAQTTEG AASEVNTHL QRIRELTVQA SNGSYSQEQL DSVQGEINQR LADIDRISEQ TDFNGVKVLS DSAKPLTLQV GANDGETITL N LSEISVKT LGLDGFNVNG KGVTQNRSAT VTDVIAQGGT LQGDGTYKAT TTFNAASAET VLSKLEDGNT VAVGGGATYT YD AAKGNFT YTKTVDTTVG ADVTALANKI KPSSGTISGS YEISTGKSAS FDVDAAGKIT IGGNAAFLNA DGELTTNDAS GAL TQATLD DVLTSVGTEA NSSVTIGGTK YSHSAADELS YTAVATTADV LSAMGSSTAV STVTLGSGIT SAAVTFAIAT TDSN NTWVD NKGELTDIQT FDTSYKINAD TGEVTVVGDN SATAGQYASA DGAKVLVGSD GKLTTETTSA GDKTTDPLKT LDAAF TKLD KLTGELGAVQ NRLESTIANL NNVVNNLSSA RSRIQDADYA TEVSNMSKAQ ILQQAGTSVL AQANQVPQTV LSLLR

UniProtKB: Flagellin

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 18.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -98.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 200000
Startup modelType of model: PDB ENTRY
Final angle assignmentType: NOT APPLICABLE

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