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- EMDB-48460: Structure of the middle part of the bacteriophage T4 tail -

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Basic information

Entry
Database: EMDB / ID: EMD-48460
TitleStructure of the middle part of the bacteriophage T4 tail
Map data3-fold-symmetric reconstruction focused on the middle part of the phage tail
Sample
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: gp18, tail sheath protein
    • Protein or peptide: gp19, tail tube protein
Keywordsbacteriophage T4 / contractile phage tail / sheath protein / tail tube protein / VIRUS / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / structural molecule activity
Similarity search - Function
: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain ...: / Tail sheath protein Gp18-like domain I / : / Tail sheath protein Gp18 domain III N-terminal region / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / : / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein central domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Tail tube protein / Tail sheath protein
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L ...Fokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L / Fang Q / Kuhn R / Rao VB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081726 United States
CitationJournal: Nat Commun / Year: 2026
Title: In situ structures of the portal-neck-tail complex of bacteriophage T4 inform a viral genome positioning mechanism.
Authors: Andrei Fokine / Jingen Zhu / Thomas Klose / Frank Vago / Charles-Adrien Arnaud / Zhiqing Wang / Baldeep Khare / Michael G Rossmann / Zhenguo Chen / Lei Sun / Qianglin Fang / Richard J Kuhn / Venigalla B Rao /
Abstract: The post-genome packaging mechanisms that govern the assembly of an infectious virion are poorly understood in bacteriophages and other viruses. Here, our near-atomic resolution cryo-EM structural ...The post-genome packaging mechanisms that govern the assembly of an infectious virion are poorly understood in bacteriophages and other viruses. Here, our near-atomic resolution cryo-EM structural analyses uncovered an assembly- and conformation-driven genome positioning mechanism in the tailed bacteriophage T4. We show that following headful packaging, which generates a pressurized head, a global conformational change occurs in the portal structure, probably triggering packaging termination and ejection of the packaging motor. Our high-resolution structures of the neck of the virion further show that the neck undergoes conformational changes upon docking of a pre-assembled tail onto the sealed neck, which then opens a genome-gate. Driven by the pressure of the packaged DNA, the genome travels through open neck channels, binds and compresses the resident tape-measure protein, and halts at the bottom of the second topmost disk of the tail tube. Pressure-suspended within the virion's innermost tunnel and secured by a baseplate plug, the genome remains poised to flow through the tunnel into a host cell upon receiving the host receptor recognition signal.
History
DepositionDec 26, 2024-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48460.png

Downloads & links

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Map

FileDownload / File: emd_48460.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3-fold-symmetric reconstruction focused on the middle part of the phage tail
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.62 Å/pix.
x 400 pix.
= 646.4 Å		1.62 Å/pix.
x 400 pix.
= 646.4 Å		1.62 Å/pix.
x 400 pix.
= 646.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.616 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.058421735 - 0.09635798
Average (Standard dev.)0.000017207425 (±0.004848805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 646.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48460_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48460_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48460_half_map_2.map
Annotationhalf map A
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 T4

EntireName: Escherichia phage T4 (virus)
Components
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: gp18, tail sheath protein
    • Protein or peptide: gp19, tail tube protein

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Supramolecule #1: Escherichia phage T4

SupramoleculeName: Escherichia phage T4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2681598 / Sci species name: Escherichia phage T4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli) / Strain: B

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Macromolecule #1: gp18, tail sheath protein

MacromoleculeName: gp18, tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 84 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 71.348625 KDa
SequenceString: MTLLSPGIEL KETTVQSTVV NNSTGTAALA GKFQWGPAFQ IKQVTNEVDL VNTFGQPTAE TADYFMSAMN FLQYGNDLRV VRAVDRDTA KNSSPIAGNI EYTISTPGSN YAVGDKITVK YVSDDIETEG KITEVDADGK IKKINIPTAK IIAKAKEVGE Y PTLGSNWT ...String:
MTLLSPGIEL KETTVQSTVV NNSTGTAALA GKFQWGPAFQ IKQVTNEVDL VNTFGQPTAE TADYFMSAMN FLQYGNDLRV VRAVDRDTA KNSSPIAGNI EYTISTPGSN YAVGDKITVK YVSDDIETEG KITEVDADGK IKKINIPTAK IIAKAKEVGE Y PTLGSNWT AEISSSSSGL AAVITLGKII TDSGILLAEI ENAEAAMTAV DFQANLKKYG IPGVVALYPG ELGDKIEIEI VS KADYAKG ASALLPIYPG GGTRASTAKA VFGYGPQTDS QYAIIVRRND AIVQSVVLST KRGGKDIYDS NIYIDDFFAK GGS EYIFAT AQNWPEGFSG ILTLSGGLSS NAEVTAGDLM EAWDFFADRE SVDVQLFIAG SCAGESLETA STVQKHVVSI GDVR QDCLV LCSPPRETVV GIPVTRAVDN LVNWRTAAGS YTDNNFNISS TYAAIDGNYK YQYDKYNDVN RWVPLAADIA GLCAR TDNV SQTWMSPAGY NRGQILNVIK LAIETRQAQR DRLYQEAINP VTGTGGDGYV LYGDKTATSV PSPFDRINVR RLFNML KTN IGRSSKYRLF ELNNAFTRSS FRTETAQYLQ GIKALGGIYE YRVVCDTTNN TPSVIDRNEF VATFYIQPAR SINYITL NF VATATGADFD ELTGLAG

UniProtKB: Tail sheath protein

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Macromolecule #2: gp19, tail tube protein

MacromoleculeName: gp19, tail tube protein / type: protein_or_peptide / ID: 2 / Number of copies: 78 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 18.479613 KDa
SequenceString:
MFVDDVTRAF ESGDFARPNL FQVEISYLGQ NFTFQCKATA LPAGIVEKIP VGFMNRKINV AGDRTFDDWT VTVMNDEAHD ARQKFVDWQ SIAAGQGNEI TGGKPAEYKK SAIVRQYARD AKTVTKEIEI KGLWPTNVGE LQLDWDSNNE IQTFEVTLAL D YWE

UniProtKB: Tail tube 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: 7.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Ted Pella lacey carbon 400 mesh grids (catalog No: 01824) were used..

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113800
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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