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Yorodumi- EMDB-7033: Emptied phiX174 complexed with lipopolysaccharides after DNA ejection -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7033 | |||||||||
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Title | Emptied phiX174 complexed with lipopolysaccharides after DNA ejection | |||||||||
Map data | Emptied phiX174 complexed with lipopolysaccharides after DNA ejection, low pass-filtered to 8 Angstrom resolution | |||||||||
Sample |
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Biological species | Enterobacteria phage phiX174 isolate Sanger (virus) / Salmonella enterica (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.9 Å | |||||||||
Authors | Rossmann MG / Sun Y / Klose T / Roznowski A / Fane BA / Pollack L / Tokuda J / Mauney A | |||||||||
Citation | Journal: Nature / Year: 2014 Title: Icosahedral bacteriophage ΦX174 forms a tail for DNA transport during infection. Authors: Lei Sun / Lindsey N Young / Xinzheng Zhang / Sergei P Boudko / Andrei Fokine / Erica Zbornik / Aaron P Roznowski / Ian J Molineux / Michael G Rossmann / Bentley A Fane / Abstract: Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on ...Prokaryotic viruses have evolved various mechanisms to transport their genomes across bacterial cell walls. Many bacteriophages use a tail to perform this function, whereas tail-less phages rely on host organelles. However, the tail-less, icosahedral, single-stranded DNA ΦX174-like coliphages do not fall into these well-defined infection processes. For these phages, DNA delivery requires a DNA pilot protein. Here we show that the ΦX174 pilot protein H oligomerizes to form a tube whose function is most probably to deliver the DNA genome across the host's periplasmic space to the cytoplasm. The 2.4 Å resolution crystal structure of the in vitro assembled H protein's central domain consists of a 170 Å-long α-helical barrel. The tube is constructed of ten α-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. Genetic and biochemical studies demonstrate that the tube is essential for infectivity but does not affect in vivo virus assembly. Cryo-electron tomograms show that tubes span the periplasmic space and are present while the genome is being delivered into the host cell's cytoplasm. Both ends of the H protein contain transmembrane domains, which anchor the assembled tubes into the inner and outer cell membranes. The central channel of the H-protein tube is lined with amide and guanidinium side chains. This may be a general property of viral DNA conduits and is likely to be critical for efficient genome translocation into the host. | |||||||||
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_7033.map.gz | 13.9 MB | EMDB map data format | |
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Header (meta data) | emd-7033-v30.xml emd-7033.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7033_fsc.xml | 6.7 KB | Display | FSC data file |
Images | emd_7033.png | 177 KB | ||
Masks | emd_7033_msk_1.map emd_7033_msk_2.map | 15.6 MB 15.6 MB | Mask map | |
Others | emd_7033_half_map_1.map.gz emd_7033_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7033 | HTTPS FTP |
-Validation report
Summary document | emd_7033_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_7033_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_7033_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7033 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7033 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_7033.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Emptied phiX174 complexed with lipopolysaccharides after DNA ejection, low pass-filtered to 8 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_7033_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_7033_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Emptied phiX174 complexed with lipopolysaccharides after DNA ejection,...
File | emd_7033_half_map_1.map | ||||||||||||
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Annotation | Emptied phiX174 complexed with lipopolysaccharides after DNA ejection, half map #1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Emptied phiX174 complexed with lipopolysaccharides after DNA ejection,...
File | emd_7033_half_map_2.map | ||||||||||||
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Annotation | Emptied phiX174 complexed with lipopolysaccharides after DNA ejection, half map #2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full phiX174 complexed with lipopolysaccharides before DNA ejection
Entire | Name: Full phiX174 complexed with lipopolysaccharides before DNA ejection |
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Components |
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-Supramolecule #1: Full phiX174 complexed with lipopolysaccharides before DNA ejection
Supramolecule | Name: Full phiX174 complexed with lipopolysaccharides before DNA ejection type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Enterobacteria phage phiX174 isolate Sanger (virus) |
Molecular weight | Theoretical: 10 KDa |
-Supramolecule #2: Lipopolysaccharides (rough strains) from Salmonella enterica sero...
Supramolecule | Name: Lipopolysaccharides (rough strains) from Salmonella enterica serotype typhimurium TV119 (Ra mutant) type: organelle_or_cellular_component / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Salmonella enterica (bacteria) / Strain: typhimurium TV119 / Location in cell: outer membrane |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3 |
Details | Mixed with LPS and incubated at 33 degrees C for 1 minute |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |