+Open data
-Basic information
Entry | Database: PDB / ID: 8ho3 | |||||||||||||||
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Title | Capsid of DT57C bacteriophage in the full state | |||||||||||||||
Components | Major head protein | |||||||||||||||
Keywords | VIRUS / Capsid / T5 / MHP | |||||||||||||||
Function / homology | Phage capsid / Phage capsid family / Major head protein Function and homology information | |||||||||||||||
Biological species | Escherichia phage DT57C (virus) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Ayala, R. / Moiseenko, A.V. / Chen, T.H. / Kulikov, E.E. / Golomidova, A.K. / Orekhov, P.S. / Street, M.A. / Sokolova, O.S. / Letarov, A.V. / Wolf, M. | |||||||||||||||
Funding support | Russian Federation, Japan, 4items
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Citation | Journal: Nat Commun / Year: 2023 Title: Nearly complete structure of bacteriophage DT57C reveals architecture of head-to-tail interface and lateral tail fibers. Authors: Rafael Ayala / Andrey V Moiseenko / Ting-Hua Chen / Eugene E Kulikov / Alla K Golomidova / Philipp S Orekhov / Maya A Street / Olga S Sokolova / Andrey V Letarov / Matthias Wolf / Abstract: The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a ...The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a different receptor (BtuB) and features highly divergent lateral tail fibers (LTF). Considerable portions of T5-like phages remain structurally uncharacterized. Here, we present the structure of DT57C determined by cryo-EM, and an atomic model of the virus, which was further explored using all-atom molecular dynamics simulations. The structure revealed a unique way of LTF attachment assisted by a dodecameric collar protein LtfC, and an unusual composition of the phage neck constructed of three protein rings. The tape measure protein (TMP) is organized within the tail tube in a three-stranded parallel α-helical coiled coil which makes direct contact with the genomic DNA. The presence of the C-terminal fragment of the TMP that remains within the tail tip suggests that the tail tip complex returns to its original state after DNA ejection. Our results provide a complete atomic structure of a T5-like phage, provide insights into the process of DNA ejection as well as a structural basis for the design of engineered phages and future mechanistic studies. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ho3.cif.gz | 649.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ho3.ent.gz | 521.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ho3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ho3_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8ho3_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ho3_validation.xml.gz | 128 KB | Display | |
Data in CIF | 8ho3_validation.cif.gz | 190.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/8ho3 ftp://data.pdbj.org/pub/pdb/validation_reports/ho/8ho3 | HTTPS FTP |
-Related structure data
Related structure data | 34920MC 8hqkC 8hqoC 8hqzC 8hreC 8hrgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 50691.398 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RSM1 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Escherichia phage DT57C / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Escherichia phage DT57C (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 67 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265376 / Symmetry type: POINT | ||||||||||||||||||||||||
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