+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20123 | |||||||||
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Title | decorated head of the phage T5 | |||||||||
Map data | empty expanded head with decoration protein | |||||||||
Sample |
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Biological species | Escherichia phage T5 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Huet A / Duda RL / Boulanger P / Conway JF | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy. Authors: Alexis Huet / Robert L Duda / Pascale Boulanger / James F Conway / Abstract: The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a ...The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 Å for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA. | |||||||||
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_20123.map.gz | 1.3 GB | EMDB map data format | |
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Header (meta data) | emd-20123-v30.xml emd-20123.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20123_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_20123.png | 312.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20123 | HTTPS FTP |
-Validation report
Summary document | emd_20123_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_20123_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_20123_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20123 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20123 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20123.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | empty expanded head with decoration protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Escherichia phage T5
Entire | Name: Escherichia phage T5 (virus) |
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Components |
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-Supramolecule #1: Escherichia phage T5
Supramolecule | Name: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10726 / Sci species name: Escherichia phage T5 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 28 MDa |
Virus shell | Shell ID: 1 / Name: D-head / Diameter: 700.0 Å / T number (triangulation number): 13 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Details: unspecified | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 1939 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |