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- PDB-8hqk: Capsid of DT57C bacteriophage in the empty state -

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Basic information

Entry
Database: PDB / ID: 8hqk
TitleCapsid of DT57C bacteriophage in the empty state
ComponentsMajor head protein
KeywordsVIRUS / Capsid / T5 / MHP
Function / homologyPhage capsid / Phage capsid family / Major head protein
Function and homology information
Biological speciesEscherichia phage DT57C (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsAyala, R. / Moiseenko, A.V. / 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
OrganizationGrant numberCountry
Russian Science Foundation21-44-07002 Russian Federation
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
Japan Society for the Promotion of Science (JSPS)20K06581 Japan
Ministry of Agriculture, Forestry and Fisheries (MAFF)20320378 Japan
CitationJournal: 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
DepositionDec 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: Major head protein
I: Major head protein
J: Major head protein
K: Major head protein
L: Major head protein
M: Major head protein


Theoretical massNumber of molelcules
Total (without water)658,98813
Polymers658,98813
Non-polymers00
Water0
1
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: Major head protein
I: Major head protein
J: Major head protein
K: Major head protein
L: Major head protein
M: Major head protein
x 60


Theoretical massNumber of molelcules
Total (without water)39,539,290780
Polymers39,539,290780
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
  • Evidence: electron microscopy, Icosahedral capsid
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: Major head protein
I: Major head protein
J: Major head protein
K: Major head protein
L: Major head protein
M: Major head protein
x 5


  • icosahedral pentamer
  • 3.29 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)3,294,94165
Polymers3,294,94165
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major head protein
B: Major head protein
C: Major head protein
D: Major head protein
E: Major head protein
F: Major head protein
G: Major head protein
H: Major head protein
I: Major head protein
J: Major head protein
K: Major head protein
L: Major head protein
M: Major head protein
x 6


  • icosahedral 23 hexamer
  • 3.95 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)3,953,92978
Polymers3,953,92978
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major head 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia phage DT57C / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Escherichia phage DT57C (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 67 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameCategory
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27507 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00692748
ELECTRON MICROSCOPYf_angle_d0.542125348
ELECTRON MICROSCOPYf_dihedral_angle_d4.30312870
ELECTRON MICROSCOPYf_chiral_restr0.04314506
ELECTRON MICROSCOPYf_plane_restr0.00316059

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