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

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Basic information

Entry
Database: EMDB / ID: 6876
TitleCryo-EM structure of Methanoccus maripaludis archaellum
Map dataMethanococcus maripaludis archaellum cryo-EM reconstruction
SampleM.maripaludis archaellin FlaB1 filament:
Flagellin
Function / homologyFlagellin, archaea / Flagellin/pilin, N-terminal / Archaebacterial flagellin / archaeal-type flagellum / structural molecule activity / integral component of membrane / Flagellin
Function and homology information
SourceMethanococcus maripaludis S2 (archaea) / Methanococcus maripaludis (strain S2 / LL) (archaea)
Methodhelical reconstruction / cryo EM / 4 Å resolution
AuthorsMeshcheryakov VA / Shibata S / Schreiber MT / Villar-Briones A / Jarrell KF / Aizawa S / Wolf M
CitationJournal: To Be Published
Title: Cryo-EM structure of Methanoccus maripaludis archaellum
Authors: Meshcheryakov VA / Shibata S / Schreiber MT / Villar-Briones A / Jarrell KF / Aizawa S / Wolf M
Validation ReportPDB-ID: 5z1l

SummaryFull reportAbout validation report
DateDeposition: Dec 26, 2017 / Header (metadata) release: Feb 13, 2019 / Map release: Feb 13, 2019 / Last update: Feb 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • 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

Downloads & links

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Map

Fileemd_6876.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
1.41 Å/pix.
= 180.48 Å
128 pix
1.41 Å/pix.
= 180.48 Å
128 pix
1.41 Å/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
Contour Level:3.0 (by author), 3 (movie #1):
Minimum - Maximum-11.208774 - 14.403278999999999
Average (Standard dev.)-0.000000002624336 (0.9999997)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64.0-64.0-64.0
Limit63.063.063.0
Spacing128128128
CellA=B=C: 180.48 Å
α=β=γ: 90.0 deg.

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/NZ
NX/NY/NZ
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 / Number of components: 2

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Component #1: protein, M.maripaludis archaellin FlaB1 filament

ProteinName: M.maripaludis archaellin FlaB1 filament / Recombinant expression: No
SourceSpecies: Methanococcus maripaludis S2 (archaea)

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Component #2: protein, Flagellin

ProteinName: Flagellin / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 21.639359 kDa
SourceSpecies: Methanococcus maripaludis (strain S2 / LL) (archaea)
Strain: S2 / LL

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: .8 mg/ml / pH: 7
Support filmGatan Solarus
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 289 K / Humidity: 100 % / Details: 3 second blot, 3.5uL.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: nanoprobe, parallel beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 96 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal), 47619.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1500.0 - -2500.0 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 77.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2000 / Sampling size: 5 microns

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Image processing

ProcessingMethod: helical reconstruction
Details: frame alignment and integration with motioncor2 incl. dose weighting and 2x Fourier cropping
3D reconstructionAlgorithm: FOURIER SPACE / Software: SPRING / CTF correction: deconvolution in SPRING / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: segmentrefine3d

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

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