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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5947 | |||||||||
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Title | Bacteriophage CUS-3 capsid icosahedral reconstruction | |||||||||
![]() | Bacteriophage CUS-3 capsid icosahedral reconstruction | |||||||||
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![]() | mature virion / capsid only / icosahedrally averaged | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
![]() | Parent KN / Tang J / Cardone G / Gilcrease EB / Janssen ME / Olson NH / Casjens SR / Baker TS | |||||||||
![]() | ![]() Title: Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain. Authors: Kristin N Parent / Jinghua Tang / Giovanni Cardone / Eddie B Gilcrease / Mandy E Janssen / Norman H Olson / Sherwood R Casjens / Timothy S Baker / ![]() Abstract: CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions ...CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the "HK97-fold" shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain ("I-domain"), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphology of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. | |||||||||
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 | ![]() | 602.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
Images | ![]() | 147.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.2 KB | Display | ![]() |
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Full document | ![]() | 77.3 KB | Display | |
Data in XML | ![]() | 494 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Bacteriophage CUS-3 capsid icosahedral reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 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 : CUS-3 virion, icosahedrally averaged
Entire | Name: CUS-3 virion, icosahedrally averaged |
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Components |
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-Supramolecule #1000: CUS-3 virion, icosahedrally averaged
Supramolecule | Name: CUS-3 virion, icosahedrally averaged / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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-Supramolecule #1: Enterobacteria phage CUS-3
Supramolecule | Name: Enterobacteria phage CUS-3 / type: virus / ID: 1 / NCBI-ID: 539221 / Sci species name: Enterobacteria phage CUS-3 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 690 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.6 / Details: 10 mM Tris, 10 mM MgCl2 |
Grid | Details: 400 mesh R2/2 Quantifoil, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 5 sec before plunging. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 89 K / Max: 91 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at the magnification used to collect data. |
Date | Sep 1, 2013 |
Image recording | Category: CCD / Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) / Digitization - Sampling interval: 6 µm / Number real images: 419 / Average electron dose: 23 e/Å2 Details: The data were collected on the DE12 camera under control of the automated acquisition software, LEGINON. |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 4.08 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
Details | Auto3dem was used for refinement. |
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CTF correction | Details: each micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: OTHER / Software - Name: Auto3dem, RobEM, autopp Details: 28 frames total were collected for each image (35 e-/A2 total dose). Only 15 were used in the final reconstruction (18e-/A2 dose). Number images used: 7766 |