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- EMDB-3746: The flagellin of Pyrococcus furiosus -

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Basic information

Entry
Database: EMDB / ID: EMD-3746
TitleThe flagellin of Pyrococcus furiosus
Map datahelical segment of the Pyrococcus furiosus archaellum
Sample
  • Complex: archaellum
    • Protein or peptide: Flagellin
Function / homologyarchaeal-type flagellum / Flagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / Flagellin
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDaum B / Vonck J / Bellack A / Chaudhuri P / Reichelt R / Albers S-V / Rachel R / Kuehlbrandt W
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
DepositionMay 31, 2017-
Header (metadata) releaseJun 7, 2017-
Map releaseJul 5, 2017-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0344
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0344
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5o4u
  • Surface level: 0.0344
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5o4u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3746.png

Downloads & links

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Map

FileDownload / File: emd_3746.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhelical segment of the Pyrococcus furiosus archaellum
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.0344 / Movie #1: 0.0344
Minimum - Maximum-0.15379982 - 0.21714751
Average (Standard dev.)0.00059139624 (±0.013378559)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 224.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z224.000224.000224.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1540.2170.001

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Supplemental data

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Half map: half map 1 for helical segment of the Pyrococcus furiosus archaellum

Fileemd_3746_half_map_1.map
Annotationhalf map 1 for helical segment of the Pyrococcus furiosus archaellum
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2 for helical segment of the Pyrococcus furiosus archaellum

Fileemd_3746_half_map_2.map
Annotationhalf map 2 for helical segment of the Pyrococcus furiosus archaellum
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : archaellum

EntireName: archaellum
Components
  • Complex: archaellum
    • Protein or peptide: Flagellin

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Supramolecule #1: archaellum

SupramoleculeName: archaellum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: helical fragment of the archaellum
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 21.7 KDa

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 22.28335 KDa
SequenceString: MAKKGAVGIG TLIVFIAMVL VAAVAAAVLI QTSGYLQQKS QATGRETTQE VASGIKVLSV VGKTDSNKTY VEKLAIYISP NAGSEGIDL NNTRVVLSNG TVQAVLKYEK TAYHKGAVGD VFNASTAWNL SNTNFGIIVL QDADNSVDQN YPTLNKGDIV V ITVKVGEG ...String:
MAKKGAVGIG TLIVFIAMVL VAAVAAAVLI QTSGYLQQKS QATGRETTQE VASGIKVLSV VGKTDSNKTY VEKLAIYISP NAGSEGIDL NNTRVVLSNG TVQAVLKYEK TAYHKGAVGD VFNASTAWNL SNTNFGIIVL QDADNSVDQN YPTLNKGDIV V ITVKVGEG NGVFGKGIPP RTKITGKVIP EFGAPGVIEF TTPSTYTSEV IELQ

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III / Details: blotting for 7-10 seconds.

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 44642 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 297 / Average exposure time: 8.0 sec. / Average electron dose: 60.0 e/Å2

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Image processing

Segment selectionNumber selected: 74823
Software:
Namedetails
EMANHelixboxer, 4712 helices selected
RELION (ver. 2.0)74823 overlapping segments
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 108 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 13965
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5tfy


Chain - Chain ID: A / Details: Some built de novo, some based on 5TFY
Output model

PDB-5o4u:
The flagellin of Pyrococcus furiosus

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