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- EMDB-3760: Sub-tomogram average of polar cap-associated hexameric protein ar... -

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Basic information

Entry
Database: EMDB / ID: EMD-3760
TitleSub-tomogram average of polar cap-associated hexameric protein array from Pyrococcus furiosus
Map dataHexameric protein array associated with the polar cap in Pyrococcus furiosus
Sample
  • Complex: Pyrococcus furiosus cells
Biological speciesPyrococcus furiosus (archaea)
Methodsubtomogram averaging / cryo EM / Resolution: 49.0 Å
AuthorsDaum B
CitationJournal: Elife / Year: 2017
Title: Structure and organisation of the archaellum machinery.
Authors: Bertram Daum / Janet Vonck / Annett Bellack / Paushali Chaudhury / Robert Reichelt / Sonja-Verena Albers / Reinhard Rachel / Werner Kühlbrandt /
Abstract: The archaellum is the macromolecular machinery that Archaea use for propulsion or surface adhesion, enabling them to proliferate and invade new territories. The molecular composition of the ...The archaellum is the macromolecular machinery that Archaea use for propulsion or surface adhesion, enabling them to proliferate and invade new territories. The molecular composition of the archaellum and of the motor that drives it appears to be entirely distinct from that of the functionally equivalent bacterial flagellum and flagellar motor. Yet, the structure of the archaellum machinery is scarcely known. Using combined modes of electron cryo-microscopy (cryoEM), we have solved the structure of the archaellum filament at 4.2 Å resolution and visualise the architecture and organisation of its motor complex . This allows us to build a structural model combining the archaellum and its motor complex, paving the way to a molecular understanding of archaeal swimming motion.
History
DepositionJun 13, 2017-
Header (metadata) releaseJun 28, 2017-
Map releaseJul 12, 2017-
UpdateMar 28, 2018-
Current statusMar 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0216
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3760.png

Downloads & links

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Map

FileDownload / File: emd_3760.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHexameric protein array associated with the polar cap in Pyrococcus furiosus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.8 Å/pix.
x 80 pix.
= 864. Å		10.8 Å/pix.
x 80 pix.
= 864. Å		10.8 Å/pix.
x 80 pix.
= 864. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0216 / Movie #1: 0.0216
Minimum - Maximum-0.30370003 - 0.23662
Average (Standard dev.)-0.038005464 (±0.03726913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 864.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.810.810.8
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z864.000864.000864.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.3040.237-0.038

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Supplemental data

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Sample components

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Entire : Pyrococcus furiosus cells

EntireName: Pyrococcus furiosus cells
Components
  • Complex: Pyrococcus furiosus cells

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Supramolecule #1: Pyrococcus furiosus cells

SupramoleculeName: Pyrococcus furiosus cells / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pyrococcus furiosus (archaea)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Detailsfrozen-hydrated cell suspension

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: Gatan Tridem
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 41000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 49.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: PEET (ver. 1.10) / Number subtomograms used: 57
ExtractionNumber tomograms: 50 / Number images used: 57 / Method: sub-volumes picked manually / Software - Name: PEET (ver. 1.10)
Details: sub-volumes were picked manually in 3Dmod and extracted using PEET
Final angle assignmentType: NOT APPLICABLE

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