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- EMDB-34952: Neck of DT57C bacteriophage in the full state -

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Basic information

Entry
Database: EMDB / ID: EMD-34952
TitleNeck of DT57C bacteriophage in the full state
Map data
Sample
  • Virus: Tequintavirus DT57C
    • Protein or peptide: Portal protein
    • Protein or peptide: Head completion protein
    • Protein or peptide: Tail terminator protein
    • Protein or peptide: Tape measure protein
KeywordsNeck / Portal / T5 / VIRUS / VIRAL PROTEIN
Function / homologyBacteriophage/Gene transfer agent portal protein / Phage portal protein / viral capsid / Head completion protein / Portal protein / Tape measure protein / Tail terminator protein
Function and homology information
Biological speciesEscherichia phage DT57C (virus) / Tequintavirus DT57C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAyala R / Moiseenko AV / Chen TH / Kulikov EE / Golomidova AK / Orekhov PS / Street MA / Sokolova OS / Letarov AV / Wolf M
Funding support Russian Federation, Japan, 4 items
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, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34952.png

Downloads & links

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Map

FileDownload / File: emd_34952.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.4 Å/pix.
x 300 pix.
= 420. Å		1.4 Å/pix.
x 300 pix.
= 420. Å		1.4 Å/pix.
x 300 pix.
= 420. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.1
Minimum - Maximum-9.474767 - 31.962872000000001
Average (Standard dev.)-0.01705147 (±0.97205377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34952_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_34952_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_34952_half_map_2.map
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Sample components

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Entire : Tequintavirus DT57C

EntireName: Tequintavirus DT57C
Components
  • Virus: Tequintavirus DT57C
    • Protein or peptide: Portal protein
    • Protein or peptide: Head completion protein
    • Protein or peptide: Tail terminator protein
    • Protein or peptide: Tape measure protein

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Supramolecule #1: Tequintavirus DT57C

SupramoleculeName: Tequintavirus DT57C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1567006 / Sci species name: Tequintavirus DT57C / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 45.408574 KDa
SequenceString: MGFKSWITEK LNPGQRIIRD MEPVSHRTNR KPFTTGQAYS KIEILNRTAN MVIDSAAECS YTVGDKYNIV TYANGVKTKT LDTLLNVRP NPFMDISTFR RLVVTDLLFE GCAYIYWDGT SLYHVPAALM QVEADANKFI KKFIFNNQIN YRVDEIIFIK D NSYVCGTN ...String:
MGFKSWITEK LNPGQRIIRD MEPVSHRTNR KPFTTGQAYS KIEILNRTAN MVIDSAAECS YTVGDKYNIV TYANGVKTKT LDTLLNVRP NPFMDISTFR RLVVTDLLFE GCAYIYWDGT SLYHVPAALM QVEADANKFI KKFIFNNQIN YRVDEIIFIK D NSYVCGTN SQISGQSRVA TVIDSLEKRS KMLNFKEKFL DNGTVIGLIL ETDEILNKKL RERKQEELQL DYNPSTGQSS VL ILDGGMK AKPYSQISSF KDLDFKEDIA GFNKSICLAF GVPQVLIDGG NNANIRPNIE LFYYMTIIPM LNKLTSSLTF FFG YKITPN TKEVAALTPD KEAEAKHLTS LVNNGIMTGN EARLELNLEP LDDEQMNRIR IPANVAGSAT GVSGQEGGRP QGST EGDKE

UniProtKB: Portal protein

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Macromolecule #2: Head completion protein

MacromoleculeName: Head completion protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 19.2039 KDa
SequenceString:
MQIITAEDYR LYGGLKRPEL ESGVEMMITA ANALITSLLG MDDADAVDQL INTKPTRKKY FLSSPSATSV TKMTINDKEI DPEQYKLYS DGVILLKFSP PEGYMDVEYT QGGFNPIPED LKLAACMLVD HWHKQDYRQA KTIGGETVTF NNTKSGIPEH I RTIIEVYR RV

UniProtKB: Head completion protein

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Macromolecule #3: Tail terminator protein

MacromoleculeName: Tail terminator protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 18.317475 KDa
SequenceString:
MDHRTSIAQA LVDRIAQQMD GSQPDEYFNN LYGNVSRQTY KFEEIREFPY VAVHIGTETG QYLPSGQQWM FLELPILVYD KEKTDIQEQ LEKLVADIKT VIDTGGNLEY TVSKPNGSTF PCEATDMSIT SVSTDEGLLA PYGLAEINVT VRYQPPRRSL R R

UniProtKB: Tail terminator protein

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Macromolecule #4: Tape measure protein

MacromoleculeName: Tape measure protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
Molecular weightTheoretical: 132.626406 KDa
SequenceString: MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP KTLYSIERAA DRAAKSLTKM QASRGMAGIT KSIDSIGAK LDDLSIAMIE VADKLEAGFD GVSRSVKVMG NDVAAATEKV QDRLYDTNRV LGGTARGFND TAGAAGRASR A IGNTSGSA ...String:
MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP KTLYSIERAA DRAAKSLTKM QASRGMAGIT KSIDSIGAK LDDLSIAMIE VADKLEAGFD GVSRSVKVMG NDVAAATEKV QDRLYDTNRV LGGTARGFND TAGAAGRASR A IGNTSGSA RGATRDFAAM AKVGGGLPLL YAAIASNIFV LQSAFEQLKL GDQLNRLEEF GVIVGTQTGT PVQSLARSLQ EA AGYAISF EEAMRQASSA SAYGFDAEQL NKFGLVARRA AAVLGVDMTD ALNRVIKGVS KQEIELLDEL GVTIRLNDAY ADY VKQLNA ANTGITYNIN SLTTFQKQQA YANAVIAEST KRFGYLDEVL RATPWEQFAA NADAALRTIQ QAAAKYLGPV IDAI NTVFY TSQASISAEA ARAQEQTNKQ IDPTNVGAVA LSLSASEEGY NKALDMYKES LDKRNKLKSE FDKRMEQADF YTKLA IRQV GEGIPAGLAT AGASEANKKF VEETAAMGLQ VARLDKEVTD STENLNAWKS AYQAAGAAAA KANPEFQKQI NLQRDT TDP GAVYDFNSTV LKGLTEQQKA YNQTKKTASD LANDIQNVAQ NTDTAAKTSA TLADAIKNIE SLSLGTGKSA DEYVKNL NL GYNTLSEMKT ASQALSEYVK LTGNETKNQL AVQQKIADVY NQTKDKEKAQ EAGRRLELQQ LEEQEAALRR VLQTNQGN K AVEREIEKIQ LEKIKLTNQG MEAQKKVKDY TDKILGVDRE IALLNNRTMT DTQYRLAQLN LELTIEKEKY EWYTKQADK QKEAEQSRRA QAQIEREIWK FHQDQQAEMT SKRQEAFENT LTSMFPLAGE MQKMEMQLDF YTQMKELTKD NANEQMRWNA EIAKTRAQM SALTAQRNAQ MQSSVGSSLG AVYTPTTGLS GEDKKFADMG NQLASYDQAI SKLSELNSEA TAVAQSMGNL A NAMIQFSQ GSLDTTSTIA VGMQTVASMI QYSTSQQVSA IDQAIAAEQK RDGKSEASKA KLKKLEAEKL KIQQDAAKKQ II IQTAVAV MQAATAVPYP FSIPLMIAAG LAGALALAQA SSASGMSSIG DSGADTASYL TLGERQKNID VSMSANAGEL SYV RGDKGI GNANSFVPRA EGGNMYPGVS YQMGEHGTEV VTPMVPMKAT PNDELKNSSN STAGRPIILN ISAMDAASFR EFAS SNSGA LRDAVELALN ENGASLKTLG NS

UniProtKB: Tape measure protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 67.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model generated in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34102
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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