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- EMDB-6876: Cryo-EM structure of Methanoccus maripaludis archaellum -

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Basic information

Entry
Database: EMDB / ID: EMD-6876
TitleCryo-EM structure of Methanoccus maripaludis archaellum
Map dataMethanococcus maripaludis archaellum cryo-EM reconstruction
Sample
  • Complex: M.maripaludis archaellin FlaB1 filament
    • Protein or peptide: Flagellin
KeywordsArchaellum / archea / flagellum / metal binding / motility / helical / PROTEIN FIBRIL
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 speciesMethanococcus maripaludis S2 (archaea) / Methanococcus maripaludis (strain S2 / LL) (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMeshcheryakov VA / Shibata S / Schreiber MT / Villar-Briones A / Jarrell KF / Aizawa S / Wolf M / Kurumizaka H
Funding support Japan, 2 items
OrganizationGrant numberCountry
JSPS Kakenhi17K17085 Japan
SPRING8Proposal No. 2014B1341 Japan
CitationJournal: EMBO Rep / Year: 2019
Title: High-resolution archaellum structure reveals a conserved metal-binding site.
Authors: Vladimir A Meshcheryakov / Satoshi Shibata / Makoto Tokoro Schreiber / Alejandro Villar-Briones / Kenneth F Jarrell / Shin-Ichi Aizawa / Matthias Wolf /
Abstract: Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are ...Many archaea swim by means of archaella. While the archaellum is similar in function to its bacterial counterpart, its structure, composition, and evolution are fundamentally different. Archaella are related to archaeal and bacterial type IV pili. Despite recent advances, our understanding of molecular processes governing archaellum assembly and stability is still incomplete. Here, we determine the structures of archaella by X-ray crystallography and cryo-EM The crystal structure of FlaB1 is the first and only crystal structure of any archaellin to date at a resolution of 1.5 Å, which is put into biological context by a cryo-EM reconstruction from archaella at 4 Å resolution created with helical single-particle analysis. Our results indicate that the archaellum is predominantly composed of FlaB1. We identify N-linked glycosylation by cryo-EM and mass spectrometry. The crystal structure reveals a highly conserved metal-binding site, which is validated by mass spectrometry and electron energy-loss spectroscopy. We show that the metal-binding site, which appears to be a widespread property of archaellin, is required for filament integrity.
History
DepositionDec 26, 2017-
Header (metadata) releaseFeb 13, 2019-
Map releaseFeb 13, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5z1l
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6876.png

Downloads & links

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Map

FileDownload / File: emd_6876.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMethanococcus maripaludis archaellum cryo-EM reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 128 pix.
= 180.48 Å		1.41 Å/pix.
x 128 pix.
= 180.48 Å		1.41 Å/pix.
x 128 pix.
= 180.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-11.208774 - 14.403278999999999
Average (Standard dev.)-0.000000002624336 (±0.9999997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 180.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.411.411.41
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z180.480180.480180.480
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-11.20914.403-0.000

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Supplemental data

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Sample components

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Entire : M.maripaludis archaellin FlaB1 filament

EntireName: M.maripaludis archaellin FlaB1 filament
Components
  • Complex: M.maripaludis archaellin FlaB1 filament
    • Protein or peptide: Flagellin

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Supramolecule #1: M.maripaludis archaellin FlaB1 filament

SupramoleculeName: M.maripaludis archaellin FlaB1 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Methanococcus maripaludis S2 (archaea)

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Methanococcus maripaludis (strain S2 / LL) (archaea)
Strain: S2 / LL
Molecular weightTheoretical: 21.639359 KDa
SequenceString: MKITEFMKSK KGASGIGTLI VFIAMVLVAA VAASVLINTS GFLQQKASTT GKESTEQVAS GLLINGITGS VGTSDVKLLA IYLAPNAGS SAIDLAQTKV MLDYNGKSVV LGYGGNQDMS SGNSSVFSND TGATATTFQV NILQDYDDSA VDNAVINKGD A VALIVDVN ...String:
MKITEFMKSK KGASGIGTLI VFIAMVLVAA VAASVLINTS GFLQQKASTT GKESTEQVAS GLLINGITGS VGTSDVKLLA IYLAPNAGS SAIDLAQTKV MLDYNGKSVV LGYGGNQDMS SGNSSVFSND TGATATTFQV NILQDYDDSA VDNAVINKGD A VALIVDVN ASFAGEIPER TAISGKVQPE FGAPGVISFT TPASYTTTLV ELQ

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

Concentration.8 mg/mL
BufferpH: 7 / Component - Formula: H2O / Component - Name: Water
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.33 kPa / Details: Gatan Solarus
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot, 3.5uL.
Detailssample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 100.0 K
Alignment procedureComa free - Residual tilt: 0.1 mrad
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Detailsnanoprobe, parallel beam illumination
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7676 pixel / Digitization - Dimensions - Height: 7420 pixel / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 2000 / Average exposure time: 12.0 sec. / Average electron dose: 96.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: -2.5 µm / Calibrated defocus min: -1.5 µm / Calibrated magnification: 47619 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsframe alignment and integration with motioncor2 incl. dose weighting and 2x Fourier cropping
Final reconstructionNumber classes used: 100 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPRING (ver. 0.84) / Number images used: 110747
Segment selectionNumber selected: 110747 / Software - Name: EMAN2 (ver. 2.1) / Software - details: e2helixboxer.py
Startup modelType of model: NONE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPRING (ver. 0.84) / Details: segmentrefine3d

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5z1l:
Cryo-EM structure of Methanoccus maripaludis archaellum

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