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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12875 | |||||||||
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Title | The archaellum of Methanocaldococcus villosus | |||||||||
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![]() | Archaellum / archaellin / Methanocaldococcus villosus / cryoEM / helical reconstruction / PROTEIN FIBRIL | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
![]() | Isupov M / Gambelli L | |||||||||
Funding support | ![]()
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![]() | ![]() Title: An archaellum filament composed of two alternating subunits. Authors: Lavinia Gambelli / Michail N Isupov / Rebecca Conners / Mathew McLaren / Annett Bellack / Vicki Gold / Reinhard Rachel / Bertram Daum / ![]() ![]() Abstract: Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of ...Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament's flexibility. #1: ![]() Title: Escaping the symmetry trap in helical reconstruction Authors: Gambelli L / Isupov MN / Daum B | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 57.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.3 KB 15.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.9 KB | Display | ![]() |
Images | ![]() | 163.6 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 502.8 KB | Display | ![]() |
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Full document | ![]() | 502.4 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ofqMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 3.3 TB Data #1: Unaligned 39-frames movies of Methanocaldococcus villosus archaella [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Archaellum
Entire | Name: Archaellum |
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Components |
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-Supramolecule #1: Archaellum
Supramolecule | Name: Archaellum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Archaellin
Macromolecule | Name: Archaellin / type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.084279 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL LCSGVTGHYV KNKGIDRIVI YITPNAGSAP IDLKQCKLF LMYDGKAVSL NFSKYDTNTV GDFTNGIKDI FNTTVVKWNN ADATSFVVVA LQDDDKSLLT NAVINKGDLA G VLVNVSAA ...String: AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL LCSGVTGHYV KNKGIDRIVI YITPNAGSAP IDLKQCKLF LMYDGKAVSL NFSKYDTNTV GDFTNGIKDI FNTTVVKWNN ADATSFVVVA LQDDDKSLLT NAVINKGDLA G VLVNVSAA FGKHVGTRER VSGYLQPEFG APAVIEFTTP AAFTSDVIEL Q |
-Macromolecule #2: Archaellin
Macromolecule | Name: Archaellin / type: protein_or_peptide / ID: 2 / Number of copies: 22 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.273643 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL QVIRVLGNHS GGKINWLAVL ISPNAGSAPI DLSQATVMI TDGTHKVIAK YNSTFFNGTL KNGGSIFEAK YNNTTALKPL FDDLPATAFG IVVLQDADTS CSKDTPVINK G DIVAICLN ...String: AIGIGTLIIF IAMVLVAAVA AAVLINTSGF LQQKAMATGK ESTEQVASGL QVIRVLGNHS GGKINWLAVL ISPNAGSAPI DLSQATVMI TDGTHKVIAK YNSTFFNGTL KNGGSIFEAK YNNTTALKPL FDDLPATAFG IVVLQDADTS CSKDTPVINK G DIVAICLN VSNTLNLKPR TKVTGAVIPE FGAPAVISFT TPATYLDTQH IIELQ |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 45 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: UNKNOWN LIGAND
Macromolecule | Name: UNKNOWN LIGAND / type: ligand / ID: 4 / Number of copies: 804 / Formula: UNL |
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Chemical component information | ![]()
ChemComp-UNL: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 7 / Component - Concentration: 5.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK III / Details: blotting time of 4 sec, -1 blot force. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2795 / Average exposure time: 1.0 sec. / Average electron dose: 37.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |