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Open data
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Basic information
Entry | ![]() | |||||||||||||||
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Title | Straight fiber of DT57C bacteriophage in the full state | |||||||||||||||
![]() | Map of the straight fiber of DT57C | |||||||||||||||
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![]() | Straight fiber / T5 / VIRUS / VIRAL PROTEIN | |||||||||||||||
Function / homology | Central straight fiber![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.5 Å | |||||||||||||||
![]() | Ayala R / Moiseenko AV / Chen TH / 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.8 KB 18.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 42.8 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() ![]() | 120.2 MB 226.6 MB 226.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hreMC ![]() 8ho3C ![]() 8hqkC ![]() 8hqoC ![]() 8hqzC ![]() 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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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Map of the straight fiber of DT57C | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Map of the straight fiber of DT57C without sharpening
File | emd_34968_additional_1.map | ||||||||||||
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Annotation | Map of the straight fiber of DT57C without sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_34968_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_34968_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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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: Central straight fiber
Macromolecule | Name: Central straight fiber / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 74.793328 KDa |
Sequence | String: MISNNAPAKM VLNSIMTGYT LAYVQHSIYT DYDVIGRSFW LKVEESIDRR DYTGVDTFFV MINNLTPSTS YEIQGAFYDS IIDSELLEA KIGINLSNET NFRTKEKPII VAARSESEPV DVGVGAPIVV VETTGEASYC TIELKSTASE DSEWVKYYIG A LGPTIKFG ...String: MISNNAPAKM VLNSIMTGYT LAYVQHSIYT DYDVIGRSFW LKVEESIDRR DYTGVDTFFV MINNLTPSTS YEIQGAFYDS IIDSELLEA KIGINLSNET NFRTKEKPII VAARSESEPV DVGVGAPIVV VETTGEASYC TIELKSTASE DSEWVKYYIG A LGPTIKFG GVPVGDYKIR ISGQVTMPDG VTVDSSGYYE YPSVFTVAYN FVPPTAPTNI AFKAARIADG KERYDARIEW DW ERGAGAN VREFLVTYIN SEEYARTGWA KAQKINVGAA RAATIISFPW KVEHTFKVSS IAWGPNRQDI TESAPATFIL NED TPLDNS FVNETGIDVN YAFIKGSMKE GEIWKQTFLI DAATGAINIG LLDEEGKAPI SFDPINRVVN VDGKVITRDI NAAN FIMTN LSGEDNPAIY TQGKSWGDNN SGIWMGMDNT SAKAKLDIGN ATQWIRYDGD VLRISSGVVI GTPNGDVDLG TGMQG KQTV FVYKLATSLP AKPLEQDYPP PGWSKTPPNR TDMTQNIYAT TGTLDPVTNR LLEGTSWSDV VQWSGTEGTI GHDGQR GPG MYSVGIAGLG GWDDGQANSF FTSNFSSAPV KYDVLTEYKS DAPGTAFTRQ WNGSGWVNPA MVLHGNMIVN GTITADK IV AGNAFLSQIG VNTIYDRAAA LSGNPEAQYK MKIDLVNGYI HIR UniProtKB: Central straight fiber |
-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 |