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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8180 | |||||||||
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Title | Cryo-EM structure of the MamK filament at 6.5 A | |||||||||
![]() | None | |||||||||
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![]() | Actin-like / Magnetosome / bacteria / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() magnetosome assembly / magnetosome membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cytoskeleton / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
![]() | Bergeron JRC / Hutto R | |||||||||
![]() | ![]() Title: Structure of the magnetosome-associated actin-like MamK filament at subnanometer resolution. Authors: Julien R C Bergeron / Rachel Hutto / Ertan Ozyamak / Nancy Hom / Jesse Hansen / Olga Draper / Meghan E Byrne / Sepehr Keyhani / Arash Komeili / Justin M Kollman / ![]() ![]() Abstract: Magnetotactic bacteria possess cellular compartments called magnetosomes that sense magnetic fields. Alignment of magnetosomes in the bacterial cell is necessary for their function, and this is ...Magnetotactic bacteria possess cellular compartments called magnetosomes that sense magnetic fields. Alignment of magnetosomes in the bacterial cell is necessary for their function, and this is achieved through anchoring of magnetosomes to filaments composed of the protein MamK. MamK is an actin homolog that polymerizes upon ATP binding. Here, we report the structure of the MamK filament at ∼6.5 Å, obtained by cryo-Electron Microscopy. This structure confirms our previously reported double-stranded, nonstaggered architecture, and reveals the molecular basis for filament formation. While MamK is closest in sequence to the bacterial actin MreB, the longitudinal contacts along each MamK strand most closely resemble those of eukaryotic actin. In contrast, the cross-strand interface, with a surprisingly limited set of contacts, is novel among actin homologs and gives rise to the nonstaggered architecture. | |||||||||
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 | ![]() | 115.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
Images | ![]() | 22.2 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jygMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.26 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 : Magnetosome-associated MamK filament
Entire | Name: Magnetosome-associated MamK filament |
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Components |
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-Supramolecule #1: Magnetosome-associated MamK filament
Supramolecule | Name: Magnetosome-associated MamK filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: ADP-bound MamK |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Actin-like ATPase
Macromolecule | Name: Actin-like ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: AMB-1 / ATCC 700264 |
Molecular weight | Theoretical: 37.65618 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSEGEGQAKN RLFLGIDLGT SHTAVMSSRG KKFLLKSVVG YPKDVIGLKL LGRPYVVGDE AFEMRSYLDI RYPLQDGVLS EISDRDIEV ARHLLTHVVK SAEPGPNDEI CAVIGVPARA SAANKALLLK MAQEVVHTAL VVSEPFMVGY GLDKLINTII V DIGAGTTD ...String: MSEGEGQAKN RLFLGIDLGT SHTAVMSSRG KKFLLKSVVG YPKDVIGLKL LGRPYVVGDE AFEMRSYLDI RYPLQDGVLS EISDRDIEV ARHLLTHVVK SAEPGPNDEI CAVIGVPARA SAANKALLLK MAQEVVHTAL VVSEPFMVGY GLDKLINTII V DIGAGTTD ICALKGTVPG PEDQVTLTKA GNYVDERLQN AILERHPELQ MNVNVACAVK EQFSFVGTPT EVASFEFRAA GK PVRADVT EPVKIACEAL MPDIIESIET LLRSFQPEYQ ATVLQNIVFA GGGSRIRGLA AYVKEKLRPF GDANVTCVKD PTF DGCRGA LRLAEELPPQ YWRQLGDVSG S UniProtKB: Actin-like protein MamK |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 14 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 14 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 53.8 Å Applied symmetry - Helical parameters - Δ&Phi: 24 ° Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8129 |
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Startup model | Type of model: OTHER / Details: featureless cylinder |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Protocol: OTHER |
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Output model | ![]() PDB-5jyg: |