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Yorodumi- EMDB-6330: 3D structure of the decameric assembly of the DNA-injection prote... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6330 | |||||||||
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Title | 3D structure of the decameric assembly of the DNA-injection protein gp12 from bacteriophage Sf6 | |||||||||
Map data | EM reconstruction of DNA injection protein decameric assembly | |||||||||
Sample |
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Keywords | bacteriophage / podovirus / DNA injection / decamer / Gram-negative / cell envelope | |||||||||
Function / homology | DNA transfer protein / DNA/protein translocase of phage P22 injectosome / Gene 12 protein Function and homology information | |||||||||
Biological species | Bacillus phage SF6 (virus) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 11.0 Å | |||||||||
Authors | Zhao H / Speir JA / Matsui T / Lin Z / Liang L / Lynn AY / Varnado B / Weiss TM / Tang L | |||||||||
Citation | Journal: PLoS One / Year: 2016 Title: Structure of a Bacterial Virus DNA-Injection Protein Complex Reveals a Decameric Assembly with a Constricted Molecular Channel. Authors: Haiyan Zhao / Jeffrey A Speir / Tsutomu Matsui / Zihan Lin / Lingfei Liang / Anna Y Lynn / Brittany Varnado / Thomas M Weiss / Liang Tang / Abstract: The multi-layered cell envelope structure of Gram-negative bacteria represents significant physical and chemical barriers for short-tailed phages to inject phage DNA into the host cytoplasm. Here we ...The multi-layered cell envelope structure of Gram-negative bacteria represents significant physical and chemical barriers for short-tailed phages to inject phage DNA into the host cytoplasm. Here we show that a DNA-injection protein of bacteriophage Sf6, gp12, forms a 465-kDa, decameric assembly in vitro. The electron microscopic structure of the gp12 assembly shows a ~150-Å, mushroom-like architecture consisting of a crown domain and a tube-like domain, which embraces a 25-Å-wide channel that could precisely accommodate dsDNA. The constricted channel suggests that gp12 mediates rapid, uni-directional injection of phage DNA into host cells by providing a molecular conduit for DNA translocation. The assembly exhibits a 10-fold symmetry, which may be a common feature among DNA-injection proteins of P22-like phages and may suggest a symmetry mismatch with respect to the 6-fold symmetric phage tail. The gp12 monomer is highly flexible in solution, supporting a mechanism for translocation of the protein through the conduit of the phage tail toward the host cell envelope, where it assembles into a DNA-injection device. | |||||||||
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_6330.map.gz | 5.5 MB | EMDB map data format | |
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Header (meta data) | emd-6330-v30.xml emd-6330.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6330_fsc.xml | 4.4 KB | Display | FSC data file |
Images | emd_6330.jpg | 298.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6330 | HTTPS FTP |
-Validation report
Summary document | emd_6330_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_6330_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_6330_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6330 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6330 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6330.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM reconstruction of DNA injection protein decameric assembly | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.73 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 : gp12 of bacteriophage Sf6
Entire | Name: gp12 of bacteriophage Sf6 |
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Components |
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-Supramolecule #1000: gp12 of bacteriophage Sf6
Supramolecule | Name: gp12 of bacteriophage Sf6 / type: sample / ID: 1000 / Details: The sample was mostly monodisperse. / Oligomeric state: decamer / Number unique components: 1 |
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Molecular weight | Experimental: 465 KDa / Theoretical: 465 KDa / Method: SDS PAGE and size exclusion |
-Macromolecule #1: product of gene 12
Macromolecule | Name: product of gene 12 / type: protein_or_peptide / ID: 1 / Name.synonym: gp12 / Number of copies: 10 / Oligomeric state: decamer / Recombinant expression: Yes |
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Source (natural) | Organism: Bacillus phage SF6 (virus) / synonym: phage Sf6 |
Molecular weight | Experimental: 46.5 KDa / Theoretical: 46.5 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pET28b |
Sequence | UniProtKB: Gene 12 protein |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.0415 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM NaPO4, 100 mM NaCl, 1 mM EDTA |
Staining | Type: NEGATIVE Details: 3 uL sample was applied onto a grid that was plasma cleaned with Ar/O2 mixture (20 sec, full power) |
Grid | Details: copper 400 mesh with carbon over vinyl |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 90 K |
Date | Aug 21, 2014 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 494 / Average electron dose: 38.89 e/Å2 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.45 µm / Nominal defocus min: -0.29 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |