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- EMDB-8405: The archaeal flagellum of Methanospirillum hungatei strain JF1. -

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Basic information

Entry
Database: EMDB / ID: EMD-8405
TitleThe archaeal flagellum of Methanospirillum hungatei strain JF1.
Map data
Sample
  • Organelle or cellular component: The flagellum of the archaea Methanospirillum hungatei
    • Protein or peptide: Flagellin
Keywordscell motility and adhesion / CELL ADHESION
Function / homologyarchaeal-type flagellum / Flagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / membrane / Flagellin
Function and homology information
Biological speciesMethanospirillum hungatei JF-1 (archaea) / Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1) (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPoweleit N / Peng G
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director1S10OD018111 United States
National Science Foundation (NSF, United States)DBI-1338135 United States
CitationJournal: Nat Microbiol / Year: 2016
Title: CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilus.
Authors: Nicole Poweleit / Peng Ge / Hong H Nguyen / Rachel R Ogorzalek Loo / Robert P Gunsalus / Z Hong Zhou /
Abstract: Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, ...Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm. The tadpole-shaped archaellin monomer has two domains, a β-barrel domain and a long, mildly kinked α-helix tail. Our structure reveals multiple post-translational modifications to the archaella, including six O-linked glycans and an unusual N-linked modification. The extensive interactions among neighbouring archaellins explain how the long but thin archaellum maintains the structural integrity required for motility-driving rotation. These extensive inter-subunit interactions and the absence of a central pore in the archaellum distinguish it from both the bacterial flagellum and type IV pili.
History
DepositionOct 13, 2016-
Header (metadata) releaseDec 7, 2016-
Map releaseDec 7, 2016-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tfy
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tfy
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5tfy
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8405.png

Downloads & links

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Map

FileDownload / File: emd_8405.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å		1.3 Å/pix.
x 256 pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0303 / Movie #1: 0.018
Minimum - Maximum-0.022486534 - 0.0426328
Average (Standard dev.)-0.0000074255076 (±0.0031979624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0220.043-0.000

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Supplemental data

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Sample components

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Entire : The flagellum of the archaea Methanospirillum hungatei

EntireName: The flagellum of the archaea Methanospirillum hungatei
Components
  • Organelle or cellular component: The flagellum of the archaea Methanospirillum hungatei
    • Protein or peptide: Flagellin

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Supramolecule #1: The flagellum of the archaea Methanospirillum hungatei

SupramoleculeName: The flagellum of the archaea Methanospirillum hungatei
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanospirillum hungatei JF-1 (archaea) / Strain: JF1
Molecular weightTheoretical: 20.048 kDa/nm

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Methanospirillum hungatei JF-1 (strain ATCC 27890 / DSM 864 / NBRC 100397 / JF-1) (archaea)
Strain: ATCC 27890 / DSM 864 / NBRC 100397 / JF-1
Molecular weightTheoretical: 17.524129 KDa
SequenceString:
FSGLEAAIVL IAFVVVAAVF SYVMLGAGFF ATQKSQEVTY SGMKQATSNL ILDGMIYGSY SKGGSGLAQL YFYVKVPEGG ETQDLKYVT YLWTKENKAV TTLTSITPTN QQLNPGARVK VTITAPTGYK PIAGQKFVLE IKPKTGASTI VTRTLSDGYN G GVII

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: 7.2
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
50.0 mMC4H11NO3Tris
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 1 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 3-13 / Number grids imaged: 2 / Average exposure time: 0.25 sec. / Average electron dose: 2.667 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: 5.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 108 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.33 CUT-OFF / Number images used: 90118
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 200
Output model

PDB-5tfy:
The archaeal flagellum of Methanospirillum hungatei strain JF1.

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