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- EMDB-66505: Phage T4 sheath in post-tail-contraction state (genome-full particle) -

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Basic information

Entry
Database: EMDB / ID: EMD-66505
TitlePhage T4 sheath in post-tail-contraction state (genome-full particle)
Map data
Sample
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Tail tube protein gp19
    • Protein or peptide: Tail tube terminator protein
KeywordsBacteriophage / Myovirus / Phage T4 / tail contraction / phage neck complex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail / 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 terminator protein / Tail sheath protein / Tail tube protein gp19
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsShao Q / Dong J / Wang A / Hu H / Yue J / Li H / Li Y / Zhang Q / Liu J / Sun L ...Shao Q / Dong J / Wang A / Hu H / Yue J / Li H / Li Y / Zhang Q / Liu J / Sun L / Fokine A / Rao VB / Tao P / Fang Q
Funding support China, United States, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371285 China
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI175340 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DP1DA060580 United States
National Science Foundation (NSF, United States)MCB-0923873 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110243 United States
National Institutes of Health/Office of the Director1S10OD023603-01A1 United States
CitationJournal: J Mol Biol / Year: 2026
Title: Cryo-EM Structures of Phage T4 Infection Intermediate.
Authors: Qianqian Shao / Junhua Dong / Aohan Wang / Hongli Hu / Jian Yue / Hongmei Li / Yinyin Li / Qinfen Zhang / Jun Liu / Lei Sun / Andrei Fokine / Venigalla B Rao / Pan Tao / Qianglin Fang /
Abstract: Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. ...Myophage is endowed with a sophisticated contractile tail and infection machinery. However, the mechanisms of host recognition, signal transduction, and genome delivery remain poorly understood. Here, we capture a pre-genome-release intermediate of myophage T4 and determine its structure by cryo-electron microscopy. Comparative analysis of this tail-contracted, pre-genome-release intermediate structure with the mature T4 virion and the tail-contracted, post-genome-release structure reveals structural transitions in the tail, tape-measure protein (TMP), baseplate, and long tail fibers that drive genome delivery. Our findings further suggest that tail sheath contraction is coupled to a coordinated repositioning of the viral DNA-TMP complex, potentially facilitating genome translocation via charge-mediated interactions. It appears that the expelled TMP may further reorganize into a putative transmembrane complex that supports genome delivery into the host cytosol.
History
DepositionOct 9, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66505.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 512 pix.
= 838.656 Å		1.64 Å/pix.
x 512 pix.
= 838.656 Å		1.64 Å/pix.
x 512 pix.
= 838.656 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0337
Minimum - Maximum-0.0998447 - 0.16657533
Average (Standard dev.)-0.000012866031 (±0.008227857)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 838.656 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66505_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_66505_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66505_half_map_2.map
Projections & Slices
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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: Tail sheath protein
    • Protein or peptide: Tail tube protein gp19
    • Protein or peptide: Tail tube terminator 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)

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Macromolecule #1: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 23 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 71.391453 KDa
SequenceString: MTLLSPGIEL KETTVQSTVV NNSTGTAALA GKFQWGPAFQ IKQVTNEVDL VNTFGQPTAE TADYFMSAMN FLQYGNDLRV VRAVDRDTA KNSSPIAGNI DYTISTPGSN YAVGDKITVK YVSDDIETEG KITEVDADGK IKKINIPTGK NYAKAKEVGE Y PTLGSNWT ...String:
MTLLSPGIEL KETTVQSTVV NNSTGTAALA GKFQWGPAFQ IKQVTNEVDL VNTFGQPTAE TADYFMSAMN FLQYGNDLRV VRAVDRDTA KNSSPIAGNI DYTISTPGSN YAVGDKITVK YVSDDIETEG KITEVDADGK IKKINIPTGK NYAKAKEVGE Y PTLGSNWT AEISSSSSGL AAVITLGKII TDSGILLAEI ENAEAAMTAV DFQANLKKYG IPGVVALYPG ELGDKIEIEI VS KADYAKG ASALLPIYPG GGTRASTAKA VFGYGPQTDS QYAIIVRRND AIVQSVVLST KRGEKDIYDS NIYIDDFFAK GGS EYIFAT AQNWPEGFSG ILTLSGGLSS NAEVTAGDLM EAWDFFADRE SVDVQLFIAG SCAGESLETA STVQKHVVSI GDAR QDCLV LCSPPRETVV GIPVTRAVDN LVNWRTAAGS YTDNNFNISS TYAAIDGNHK YQYDKYNDVN RWVPLAADIA GLCAR TDNV SQTWMSPAGY NRGQILNVIK LAIETRQAQR DRLYQEAINP VTGTGGDGYV LYGDKTATSV PSPFDRINVR RLFNML KTN IGRSSKYRLF ELNNAFTRSS FRTETAQYLQ GNKALGGIYE YRVVCDTTNN TPSVIDRNEF VATFYIQPAR SINYITL NF VATATGADFD ELTGLAG

UniProtKB: Tail sheath protein

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Macromolecule #2: Tail tube protein gp19

MacromoleculeName: Tail tube protein gp19 / type: protein_or_peptide / ID: 2 / Number of copies: 10 / 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 gp19

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Macromolecule #3: Tail tube terminator protein

MacromoleculeName: Tail tube terminator protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 19.723143 KDa
SequenceString:
MSQALQQIFN QANTTNFVVS IPHSNTTSAF TLNAQSVPIP GIRIPVTDTV TGPFGLGRAQ RPGVTFEYDP LIVRFIVDEE LKSWIGMYE WMLGTSNYLT GENTAQKTGP EYITLYILDN SKTEIVMSIN FYKPWVSDLS EVEFSYTEDS DPALVCTATI P YTYFQVEK DGKIIAEV

UniProtKB: Tail tube terminator 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: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Detector mode: SUPER-RESOLUTION / #0 - Number real images: 2276 / #0 - Average exposure time: 8.0 sec. / #0 - Average electron dose: 40.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 (6k x 4k) / #1 - Number real images: 5090 / #1 - Average exposure time: 8.0 sec. / #1 - Average electron dose: 59.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 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

Image recording ID1
Particle selectionNumber selected: 116671
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 40108
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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