+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2068 | |||||||||
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Title | Alp12 filament structure | |||||||||
Map data | Reconstruction of the Alp12 filament | |||||||||
Sample |
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Keywords | Alp12 / actin-like protein / Clostridium tetani | |||||||||
Function / homology | Actin-like protein, N-terminal / Actin like proteins N terminal domain / ParM-like / ATPase, nucleotide binding domain / Actin-like protein N-terminal domain-containing protein Function and homology information | |||||||||
Biological species | Clostridium tetani (bacteria) | |||||||||
Method | helical reconstruction / negative staining / Resolution: 19.7 Å | |||||||||
Authors | Popp D / Narita A / Lee LJ / Ghoshdastider U / Xue B / Srinivasan R / Balasubramanian MK / Tanaka T / Robinson RC | |||||||||
Citation | Journal: J Biol Chem / Year: 2012 Title: Novel actin-like filament structure from Clostridium tetani. Authors: David Popp / Akihiro Narita / Lin Jie Lee / Umesh Ghoshdastider / Bo Xue / Ramanujam Srinivasan / Mohan K Balasubramanian / Toshitsugu Tanaka / Robert C Robinson / Abstract: Eukaryotic F-actin is constructed from two protofilaments that gently wind around each other to form a helical polymer. Several bacterial actin-like proteins (Alps) are also known to form F-actin- ...Eukaryotic F-actin is constructed from two protofilaments that gently wind around each other to form a helical polymer. Several bacterial actin-like proteins (Alps) are also known to form F-actin-like helical arrangements from two protofilaments, yet with varied helical geometries. Here, we report a unique filament architecture of Alp12 from Clostridium tetani that is constructed from four protofilaments. Through fitting of an Alp12 monomer homology model into the electron microscopy data, the filament was determined to be constructed from two antiparallel strands, each composed of two parallel protofilaments. These four protofilaments form an open helical cylinder separated by a wide cleft. The molecular interactions within single protofilaments are similar to F-actin, yet interactions between protofilaments differ from those in F-actin. The filament structure and assembly and disassembly kinetics suggest Alp12 to be a dynamically unstable force-generating motor involved in segregating the pE88 plasmid, which encodes the lethal tetanus toxin, and thus a potential target for drug design. Alp12 can be repeatedly cycled between states of polymerization and dissociation, making it a novel candidate for incorporation into fuel-propelled nanobiopolymer machines. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2068.map.gz | 1 MB | EMDB map data format | |
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Header (meta data) | emd-2068-v30.xml emd-2068.xml | 10.2 KB 10.2 KB | Display Display | EMDB header |
Images | emd-2068.jpg | 60.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2068 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2068 | HTTPS FTP |
-Validation report
Summary document | emd_2068_validation.pdf.gz | 183.9 KB | Display | EMDB validaton report |
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Full document | emd_2068_full_validation.pdf.gz | 183.1 KB | Display | |
Data in XML | emd_2068_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2068 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2068 | HTTPS FTP |
-Related structure data
Related structure data | 4apwMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2068.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the Alp12 filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Filament structure of an actin-like protein, Alp12, in Clostridiu...
Entire | Name: Filament structure of an actin-like protein, Alp12, in Clostridium tetani |
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Components |
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-Supramolecule #1000: Filament structure of an actin-like protein, Alp12, in Clostridiu...
Supramolecule | Name: Filament structure of an actin-like protein, Alp12, in Clostridium tetani type: sample / ID: 1000 / Oligomeric state: Helical filament / Number unique components: 1 |
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Molecular weight | Method: Sequence |
-Macromolecule #1: Alp12
Macromolecule | Name: Alp12 / type: protein_or_peptide / ID: 1 / Oligomeric state: Filament / Recombinant expression: Yes |
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Source (natural) | Organism: Clostridium tetani (bacteria) |
Molecular weight | Theoretical: 37 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pSY5 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.35 mg/mL |
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Buffer | pH: 7.5 Details: 300 mM KCl, 1 mM MgCl2, 0.5 mM DTT, 30 mM Hepes, 1 mM ATP |
Staining | Type: NEGATIVE Details: A drop of Alp12 solution was applied to grids, blotted, stained with 1 % uranyl acetate |
Grid | Details: 200 mesh copper grid with thin carbon support |
Vitrification | Cryogen name: NONE / Instrument: OTHER / Method: Negatively staining |
-Electron microscopy
Microscope | HITACHI H7600 |
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Date | Sep 6, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 31 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 100 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Details | The particles were aligned using Eos. |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 42.88 Å Applied symmetry - Helical parameters - Δ&Phi: 13.24 ° Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EOS |
CTF correction | Details: Each scanned image |