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- EMDB-25215: Cryo-EM structure of the Sinorhizobium meliloti flagellar filament -

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Basic information

Entry
Database: EMDB / ID: EMD-25215
TitleCryo-EM structure of the Sinorhizobium meliloti flagellar filament
Map data
Sample
  • Complex: Structure of the Sinorhizobium meliloti flagellar filament
    • Protein or peptide: Flagellin A
KeywordsBacteria flagellar filament / motility / flagellar polymorphism / STRUCTURAL PROTEIN
Function / homologyFlagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region / bacterial-type flagellum / structural molecule activity / extracellular region / Flagellin A
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKreutzberger MAB / Scharf BE
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510
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
DepositionOct 27, 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: 0.102
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.102
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sn9
  • Surface level: 0.102
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7sn9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25215.png

Downloads & links

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Map

FileDownload / File: emd_25215.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å		1.08 Å/pix.
x 384 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102 / Movie #1: 0.102
Minimum - Maximum-0.24497432 - 0.40379044
Average (Standard dev.)0.0030663656 (±0.03322773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 414.72003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z414.720414.720414.720
α/β/γ90.00090.00090.000
start NX/NY/NZ138136120
NX/NY/NZ121111179
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.2450.4040.003

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Supplemental data

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Sample components

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Entire : Structure of the Sinorhizobium meliloti flagellar filament

EntireName: Structure of the Sinorhizobium meliloti flagellar filament
Components
  • Complex: Structure of the Sinorhizobium meliloti flagellar filament
    • Protein or peptide: Flagellin A

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Supramolecule #1: Structure of the Sinorhizobium meliloti flagellar filament

SupramoleculeName: Structure of the Sinorhizobium meliloti flagellar filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sinorhizobium meliloti (bacteria)

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Macromolecule #1: Flagellin A

MacromoleculeName: Flagellin A / type: protein_or_peptide / ID: 1 / Number of copies: 42 / Enantiomer: LEVO
Source (natural)Organism: Sinorhizobium meliloti (bacteria)
Molecular weightTheoretical: 40.61568 KDa
Recombinant expressionOrganism: Sinorhizobium meliloti (bacteria)
SequenceString: MTSILTNNSA MAALSGVRSI SSSMEDTQSR ISSGLRVGSA SDNAAYWSIA TTMRSDNQAL SAVQDALGLG AAKVDTAYSG MESAIEVVK EIKAKLVAAT EDGVDKAKIQ EEITQLKDQL TSIADAASFS GENWLQADLS GGAVTKSVVG SFVRDGSGSV A VKKVDYSL ...String:
MTSILTNNSA MAALSGVRSI SSSMEDTQSR ISSGLRVGSA SDNAAYWSIA TTMRSDNQAL SAVQDALGLG AAKVDTAYSG MESAIEVVK EIKAKLVAAT EDGVDKAKIQ EEITQLKDQL TSIADAASFS GENWLQADLS GGAVTKSVVG SFVRDGSGSV A VKKVDYSL NANSVLFDTV GDTGILDKVY NVSQASVTLT VNTNGVESQH TVAAYSLESL TEAGAEFQGN YALQGGNSYV KV ENVWVRA ETAATGATGQ EIAATTTAAG TITADSWVVD VGNAPAANVS AGQSVANINI VGMGAAALDA LISGVDAALT DMT SAAASL GSISSRIDLQ SEFVNKLSDS IESGVGRLVD ADMNEESTRL KALQTQQQLA IQALSIANSD SQNVLSLFR

UniProtKB: Flagellin A

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 222 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 9.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 130.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16158
Startup modelType of model: OTHER / Details: Cylinder
Final angle assignmentType: NOT APPLICABLE

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