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Open data
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Basic information
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Title | Capsid of DT57C bacteriophage in the empty state | |||||||||||||||
![]() | Map of the capsid of empty DT57C bacteriophage | |||||||||||||||
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![]() | Capsid / T5 / MHP / VIRUS | |||||||||||||||
Function / homology | Phage capsid / Phage capsid family / Major head protein![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
![]() | Ayala R / Moiseenko AV / Kulikov EE / Golomidova AK / Orekhov PS / Street MA / Sokolova OS / Letarov AV / Wolf M | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
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Downloads & links
-EMDB archive
Map data | ![]() | 2.6 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 29.6 KB | Display | ![]() |
Images | ![]() | 174.3 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 2.5 GB 2.5 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hqkMC ![]() 8ho3C ![]() 8hqoC ![]() 8hqzC ![]() 8hreC ![]() 8hrgC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Map of the capsid of empty DT57C bacteriophage | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.387 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_34949_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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-Half map: Half map B
File | emd_34949_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Sample components
-Entire : Escherichia phage DT57C
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Escherichia phage DT57C
Supramolecule | Name: Escherichia phage DT57C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2681606 / Sci species name: Escherichia phage DT57C / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: Major head protein
Macromolecule | Name: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 50.691398 KDa |
Sequence | String: MTIDINKLKE ELGLGDLAKS LEGLTAAQKA QEAERMRKEQ EEKELARMNA LVSKAVGEDR QKLEQALELV KSLDEKSKKS AELFAQTVE KQQETIVGLQ DEIKSLLTAR EGRSFVGDSV AKALYGTQET FEDEVEKLVL LSYVMEKGVF ETEHGQKHLK A VNQSSSVE ...String: MTIDINKLKE ELGLGDLAKS LEGLTAAQKA QEAERMRKEQ EEKELARMNA LVSKAVGEDR QKLEQALELV KSLDEKSKKS AELFAQTVE KQQETIVGLQ DEIKSLLTAR EGRSFVGDSV AKALYGTQET FEDEVEKLVL LSYVMEKGVF ETEHGQKHLK A VNQSSSVE VSSESYETIF SQRIIRDLQK ELVVGALFEE LPMSSKILTM LVEPDAGRAT WVAASAYGSD NTTGSEVTGA LT EIHFSTY KLAAKSFITD ETEEDAIFSL LPLLRKRLIE AHAVSIEEAF MTGDGSGKPK GLLTLASEDS AKVTTEAKAD GSV LVTAKT ISKLRRKLGR HGLKLSKLVL IVSMDAYYDL LEDEEWQDVA QVGNDAVKLQ GQVGRIYGLP VVVSEYFPAK AAGK EFAVI VYKDNFVMPR QRAVTVERER QAGKQRDAYY VTQRVNLQRY FENGVVSGAY AAS UniProtKB: Major head protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |