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- PDB-8hqz: Baseplate of DT57C bacteriophage in the full state -

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Basic information

Entry
Database: PDB / ID: 8hqz
TitleBaseplate of DT57C bacteriophage in the full state
Components
  • (L-shaped tail fiber ...) x 2
  • Baseplate hub protein
  • Distal tail protein
  • Minor tail protein
  • Tail tube protein
  • Tape measure protein
KeywordsVIRAL PROTEIN / Baseplate / T5 / VIRUS
Function / homology
Function and homology information


Intramolecular chaperone auto-processing domain / Intramolecular chaperone auto-processing (ICA) domain profile. / Tip attachment protein J / Putative phage tail protein / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Distal tail protein / Tail tube protein / Baseplate hub protein / Minor tail protein / L-shaped tail fiber assembly / L-shaped tail fiber assembly / Tape measure protein
Similarity search - Component
Biological speciesEscherichia phage DT57C (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAyala, 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
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 14, 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: Baseplate hub protein
H: Distal tail protein
I: Distal tail protein
L: Minor tail protein
Q: L-shaped tail fiber assembly
R: L-shaped tail fiber assembly
S: L-shaped tail fiber assembly
T: L-shaped tail fiber assembly
d: L-shaped tail fiber assembly
e: L-shaped tail fiber assembly
f: L-shaped tail fiber assembly
k: Tape measure protein
p: Tail tube protein


Theoretical massNumber of molelcules
Total (without water)773,02013
Polymers773,02013
Non-polymers00
Water00
1
A: Baseplate hub protein
H: Distal tail protein
I: Distal tail protein
L: Minor tail protein
Q: L-shaped tail fiber assembly
R: L-shaped tail fiber assembly
S: L-shaped tail fiber assembly
T: L-shaped tail fiber assembly
d: L-shaped tail fiber assembly
e: L-shaped tail fiber assembly
f: L-shaped tail fiber assembly
k: Tape measure protein
p: Tail tube protein

A: Baseplate hub protein
H: Distal tail protein
I: Distal tail protein
L: Minor tail protein
Q: L-shaped tail fiber assembly
R: L-shaped tail fiber assembly
S: L-shaped tail fiber assembly
T: L-shaped tail fiber assembly
d: L-shaped tail fiber assembly
e: L-shaped tail fiber assembly
f: L-shaped tail fiber assembly
k: Tape measure protein
p: Tail tube protein

A: Baseplate hub protein
H: Distal tail protein
I: Distal tail protein
L: Minor tail protein
Q: L-shaped tail fiber assembly
R: L-shaped tail fiber assembly
S: L-shaped tail fiber assembly
T: L-shaped tail fiber assembly
d: L-shaped tail fiber assembly
e: L-shaped tail fiber assembly
f: L-shaped tail fiber assembly
k: Tape measure protein
p: Tail tube protein


  • complete point assembly
  • Evidence: electron microscopy
  • 2.32 MDa, 39 polymers
Theoretical massNumber of molelcules
Total (without water)2,319,06139
Polymers2,319,06139
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
2


  • Idetical with deposited unit
  • point asymmetric unit
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))

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Components

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Protein , 5 types, 6 molecules AHILkp

#1: Protein Baseplate hub protein


Mass: 107114.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RSL1
#2: Protein Distal tail protein


Mass: 22666.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RSH9
#3: Protein Minor tail protein


Mass: 34513.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RSL6
#6: Protein Tape measure protein


Mass: 132626.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RZ92
#7: Protein Tail tube protein


Mass: 50759.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RSI5

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L-shaped tail fiber ... , 2 types, 7 molecules QRSTdef

#4: Protein
L-shaped tail fiber assembly


Mass: 15384.226 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RUJ8
#5: Protein L-shaped tail fiber assembly


Mass: 113712.461 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage DT57C (virus) / References: UniProt: A0A0A7RZ88

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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 FIELD / 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

EM software
IDNameCategory
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42697 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0167635
ELECTRON MICROSCOPYf_angle_d0.84491917
ELECTRON MICROSCOPYf_dihedral_angle_d12.77724708
ELECTRON MICROSCOPYf_chiral_restr0.0510497
ELECTRON MICROSCOPYf_plane_restr0.01211952

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