+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3746 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The archaellum of Pyrococcus furiosus | |||||||||
Map data | helical segment of the Pyrococcus furiosus archaellum | |||||||||
Sample |
| |||||||||
Keywords | archaellar flagellum glycoprotein helical filament / Cell adhesion | |||||||||
Function / homology | archaeal-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 species | Pyrococcus furiosus DSM 3638 (archaea) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Daum B / Vonck J / Bellack A / Chaudhuri P / Reichelt R / Albers S-V / Rachel R / Kuehlbrandt W | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3746.map.gz | 5.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3746-v30.xml emd-3746.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3746_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_3746.png | 170.5 KB | ||
Filedesc metadata | emd-3746.cif.gz | 5.7 KB | ||
Others | emd_3746_half_map_1.map.gz emd_3746_half_map_2.map.gz | 23.4 MB 23.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3746 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3746 | HTTPS FTP |
-Validation report
Summary document | emd_3746_validation.pdf.gz | 497.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_3746_full_validation.pdf.gz | 496.4 KB | Display | |
Data in XML | emd_3746_validation.xml.gz | 12.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3746 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3746 | HTTPS FTP |
-Related structure data
Related structure data | 5o4uMC 3759C 3760C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_3746.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | helical segment of the Pyrococcus furiosus archaellum | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Half map: half map 1 for helical segment of the Pyrococcus furiosus archaellum
File | emd_3746_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 1 for helical segment of the Pyrococcus furiosus archaellum | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map 2 for helical segment of the Pyrococcus furiosus archaellum
File | emd_3746_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map 2 for helical segment of the Pyrococcus furiosus archaellum | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : archaellum
Entire | Name: archaellum |
---|---|
Components |
|
-Supramolecule #1: archaellum
Supramolecule | Name: 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 weight | Theoretical: 21.7 KDa |
-Macromolecule #1: Flagellin
Macromolecule | Name: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Pyrococcus furiosus DSM 3638 (archaea) |
Molecular weight | Theoretical: 22.28335 KDa |
Sequence | String: 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 UniProtKB: Flagellin |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III / Details: blotting for 7-10 seconds. |
-Electron microscopy
Microscope | JEOL 3200FSC |
---|---|
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 44642 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 30000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN |