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- EMDB-34973: Curved tail segment of the DT57C bacteriophage in the full state -

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Basic information

Entry
Database: EMDB / ID: EMD-34973
TitleCurved tail segment of the DT57C bacteriophage in the full state
Map dataMap of a curved segment of the tail
Sample
  • Virus: Escherichia phage DT57C (virus)
    • Protein or peptide: Tail tube protein (TTP)
    • Protein or peptide: Tape measure protein (TMP)
KeywordsTail tube / T5 / VIRUS / VIRAL PROTEIN
Biological speciesEscherichia phage DT57C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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
Other government20320378
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 15, 2022-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34973.png

Downloads & links

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Map

FileDownload / File: emd_34973.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of a curved segment of the tail
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-3.2858975 - 13.045817
Average (Standard dev.)0.025971128 (±0.51616335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_34973_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_34973_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage DT57C

EntireName: Escherichia phage DT57C (virus)
Components
  • Virus: Escherichia phage DT57C (virus)
    • Protein or peptide: Tail tube protein (TTP)
    • Protein or peptide: Tape measure protein (TMP)

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Supramolecule #1: Escherichia phage DT57C

SupramoleculeName: 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: Tail tube protein (TTP)

MacromoleculeName: Tail tube protein (TTP) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
SequenceString: MSLQLLRNTR IFVSTVKTGH DTTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAE WSFSTYILPY EDTTTGKQIV PDYMLWHALS SGKAIDLDGD TGAHNNATNF M VNFKDNAY HELAMLHIYI LTDNAWSYID SCQINQAEVN VDIEDIGRVT ...String:
MSLQLLRNTR IFVSTVKTGH DTTNTQEILV QDDISWGQDS NSTDITVNEA GPRPTRGSKR FNDSLNAAE WSFSTYILPY EDTTTGKQIV PDYMLWHALS SGKAIDLDGD TGAHNNATNF M VNFKDNAY HELAMLHIYI LTDNAWSYID SCQINQAEVN VDIEDIGRVT WSGNGNQLIP LD EQPFDPD ALGIDDETYM TIQSSYIKNK LTILKIKDMD SDKEYDIPIT GGTFTINNNI TYL TPNIMS RVNIPIGSFT GAFELTGSLT AYLNDKSLGS MELYKDLVRT LKVVNRFEIA LILG GEYDD ERPAAVLVAK QAHVNIPTIE TDDVLGTSVE FKAIPTDLDT GDEGYLGFSN KYTKT TVAN LIATGDGAET PPILVESITV KSAADATSVT NSDTLQMSVE VTPPEATNTA VTWSIS SGD AATIDAESGL LTADVSKTGE VIVKAVAKDG SGVEGTKTIT VSAGE

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Macromolecule #2: Tape measure protein (TMP)

MacromoleculeName: Tape measure protein (TMP) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage DT57C (virus)
SequenceString: MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP KTLYSIERAA DRAAKSLTK MQASRGMAGI TKSIDSIGAK LDDLSIAMIE VADKLEAGFD GVSRSVKVMG N DVAAATEK VQDRLYDTNR VLGGTARGFN DTAGAAGRAS RAIGNTSGSA ...String:
MTDKLIRELL IDVKQKGATR TAKSIENVSD ALENAAAASE LTNEQLGKMP KTLYSIERAA DRAAKSLTK MQASRGMAGI TKSIDSIGAK LDDLSIAMIE VADKLEAGFD GVSRSVKVMG N DVAAATEK VQDRLYDTNR VLGGTARGFN DTAGAAGRAS RAIGNTSGSA RGATRDFAAM AK VGGGLPL LYAAIASNIF VLQSAFEQLK LGDQLNRLEE FGVIVGTQTG TPVQSLARSL QEA AGYAIS FEEAMRQASS ASAYGFDAEQ LNKFGLVARR AAAVLGVDMT DALNRVIKGV SKQE IELLD ELGVTIRLND AYADYVKQLN AANTGITYNI NSLTTFQKQQ AYANAVIAES TKRFG YLDE VLRATPWEQF AANADAALRT IQQAAAKYLG PVIDAINTVF YTSQASISAE AARAQE QTN KQIDPTNVGA VALSLSASEE GYNKALDMYK ESLDKRNKLK SEFDKRMEQA DFYTKLA IR QVGEGIPAGL ATAGASEANK KFVEETAAMG LQVARLDKEV TDSTENLNAW KSAYQAAG A AAAKANPEFQ KQINLQRDTT DPGAVYDFNS TVLKGLTEQQ KAYNQTKKTA SDLANDIQN VAQNTDTAAK TSATLADAIK NIESLSLGTG KSADEYVKNL NLGYNTLSEM KTASQALSEY VKLTGNETK NQLAVQQKIA DVYNQTKDKE KAQEAGRRLE LQQLEEQEAA LRRVLQTNQG N KAVEREIE KIQLEKIKLT NQGMEAQKKV KDYTDKILGV DREIALLNNR TMTDTQYRLA QL NLELTIE KEKYEWYTKQ ADKQKEAEQS RRAQAQIERE IWKFHQDQQA EMTSKRQEAF ENT LTSMFP LAGEMQKMEM QLDFYTQMKE LTKDNANEQM RWNAEIAKTR AQMSALTAQR NAQM QSSVG SSLGAVYTPT TGLSGEDKKF ADMGNQLASY DQAISKLSEL NSEATAVAQS MGNLA NAMI QFSQGSLDTT STIAVGMQTV ASMIQYSTSQ QVSAIDQAIA AEQKRDGKSE ASKAKL KKL EAEKLKIQQD AAKKQIIIQT AVAVMQAATA VPYPFSIPLM IAAGLAGALA LAQASSA SG MSSIGDSGAD TASYLTLGER QKNIDVSMSA NAGELSYVRG DKGIGNANSF VPRAEGGN M YPGVSYQMGE HGTEVVTPMV PMKATPNDEL KNSSNSTAGR PIILNISAMD AASFREFAS SNSGALRDAV ELALNENGAS LKTLGNS

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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: 7.5
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 cisTEM
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 431751
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM
FSC plot (resolution estimation)

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