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- EMDB-66504: Phage T4 neck in post-tail-contraction state (genome-full particle) -

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Basic information

Entry
Database: EMDB / ID: EMD-66504
TitlePhage T4 neck in post-tail-contraction state (genome-full particle)
Map data
Sample
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: Portal protein
    • Protein or peptide: Neck protein gp13
    • Protein or peptide: Neck protein gp14
    • Protein or peptide: Tail completion protein gp15
    • Protein or peptide: Fibritin
KeywordsBacteriophage / Myovirus / Phage T4 / tail contraction / phage neck complex / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / viral portal complex / viral genome packaging / viral release from host cell / virion component / host cell plasma membrane
Similarity search - Function
Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Portal protein Gp20 / Bacteriophage T4, Gp14, neck protein / : / Bacteriophage T4-like portal protein (Gp20) / Virus neck protein / Bacteriophage T4 neck protein gp13 / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Fibritin / Neck protein gp13 / Neck protein gp14 / Tail completion protein gp15 / Portal protein
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_66504.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 400 pix.
= 655.2 Å		1.64 Å/pix.
x 400 pix.
= 655.2 Å		1.64 Å/pix.
x 400 pix.
= 655.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.07962408 - 0.13131508
Average (Standard dev.)-0.00007538033 (±0.005790471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 655.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66504_msk_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_66504_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66504_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: Portal protein
    • Protein or peptide: Neck protein gp13
    • Protein or peptide: Neck protein gp14
    • Protein or peptide: Tail completion protein gp15
    • Protein or peptide: Fibritin

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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: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 61.117082 KDa
SequenceString: MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK ...String:
MKFNVLSLFA PWAKMDERNF KDQEKEDLVS ITAPKLDDGA REFEVSSNEA ASPYNAAFQT IFGSYEPGMK TTRELIDTYR NLMNNYEVD NAVSEIVSDA IVYEDDTEVV ALNLDKSKFS PKIKNMMLDE FSDVLNHLSF QRKGSDHFRR WYVDSRIFFH K IIDPKRPK EGIKELRRLD PRQVQYVREI ITETEAGTKI VKGYKEYFIY DTAHESYACD GRMYEAGTKI KIPKAAVVYA HS GLVDCCG KNIIGYLHRA VKPANQLKLL EDAVVIYRIT RAPDRRVWYV DTGNMPARKA AEHMQHVMNT MKNRVVYDAS TGK IKNQQH NMSMTEDYWL QRRDGKAVTE VDTLPGADNT GNMEDIRWFR QALYMALRVP LSRIPQDQQG GVMFDSGTSI TRDE LTFAK FIRELQHKFE EVFLDPLKTN LLLKGIITED EWNDEINNIK IEFHRDSYFA ELKEAEILER RINMLTMAEP FIGKY ISHR TAMKDILQMT DEEIEQEAKQ IEEESKEARF QDPDQEQEDF

UniProtKB: Portal protein

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Macromolecule #2: Neck protein gp13

MacromoleculeName: Neck protein gp13 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 34.772211 KDa
SequenceString: MSGYNPQNPK ELKDVILRRL GAPIINVELT PDQIYDCIQR ALELYGEYHF DGLNKGFHVF YVGDDEERYK TGVFDLRGSN VFAVTRILR TNIGSITSMD GNATYPWFTD FLLGMAGING GMGTSCNRFY GPNAFGADLG YFTQLTSYMG MMQDMLSPIP D FWFNSANE ...String:
MSGYNPQNPK ELKDVILRRL GAPIINVELT PDQIYDCIQR ALELYGEYHF DGLNKGFHVF YVGDDEERYK TGVFDLRGSN VFAVTRILR TNIGSITSMD GNATYPWFTD FLLGMAGING GMGTSCNRFY GPNAFGADLG YFTQLTSYMG MMQDMLSPIP D FWFNSANE QLKVMGNFQK YDLIIVESWT KSYIDTNKMV GNTVGYGTVG PQDSWSLSER YNNPDHNLVG RVVGQDPNVK QG AYNNRWV KDYATALAKE LNGQILARHQ GMMLPGGVTI DGQRLIEEAR LEKEALREEL YLLDPPFGIL VG

UniProtKB: Neck protein gp13

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Macromolecule #3: Neck protein gp14

MacromoleculeName: Neck protein gp14 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 29.597836 KDa
SequenceString: MATYDKNLFA KLENRTGYSQ TNETEILNPY VNFNHYKNSQ ILADVLVAES IQMRGVECYY VPREYVSPDL IFGEDLKNKF TKAWKFAAY LNSFEGYEGA KSFFSNFGMQ VQDEVTLSIN PNLFKHQVNG KEPKEGDLIY FPMDNSLFEI NWVEPYDPFY Q LGQNAIRK ...String:
MATYDKNLFA KLENRTGYSQ TNETEILNPY VNFNHYKNSQ ILADVLVAES IQMRGVECYY VPREYVSPDL IFGEDLKNKF TKAWKFAAY LNSFEGYEGA KSFFSNFGMQ VQDEVTLSIN PNLFKHQVNG KEPKEGDLIY FPMDNSLFEI NWVEPYDPFY Q LGQNAIRK ITAGKFIYSG EEINPVLQKN EGINIPEFSE LELNAVRNLN GIHDINIDQY AEVDQINSEA KEYVEPYVVV NN RGKSFES SPFDNDFMD

UniProtKB: Neck protein gp14

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Macromolecule #4: Tail completion protein gp15

MacromoleculeName: Tail completion protein gp15 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 31.587486 KDa
SequenceString: MFGYFYNSSF RRYATLMGDL FSNIQIKRQL ESGDKFIRVP ITYASKEHFM MKLNKWTSIN SQEDVAKVET ILPRINLHLV DFSYNAPFK TNILNQNLLQ KGATSVVSQY NPSPIKMIYE LSIFTRYEDD MFQIVEQILP YFQPHFNTTM YEQFGNDIPF K RDIKIVLM ...String:
MFGYFYNSSF RRYATLMGDL FSNIQIKRQL ESGDKFIRVP ITYASKEHFM MKLNKWTSIN SQEDVAKVET ILPRINLHLV DFSYNAPFK TNILNQNLLQ KGATSVVSQY NPSPIKMIYE LSIFTRYEDD MFQIVEQILP YFQPHFNTTM YEQFGNDIPF K RDIKIVLM SAAIDEAIDG DNLSRRRIEW SLTFEVNGWM YPPVDDAEGL IRTTYTDFHA NTRDLPDGEG VFESVDSEVV PR DIDPEDW DGTVKQTFTS NVNRPTPPEP PGPRT

UniProtKB: Tail completion protein gp15

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Macromolecule #5: Fibritin

MacromoleculeName: Fibritin / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 51.909164 KDa
SequenceString: MTDIVLNDLP FVDGPPAEGQ SRISWIKNGE EILGADTQYG SEGSMNRPTV SVLRNVEVLD KNIGILKTSL ETANSDIKTI QGILDVSGD IEALAQIGIN KKDISDLKTL TSEHTEILNG TNNTVDSILA DIGPFNAEAN SVYRTIRNDL LWIKRELGQY T GQDINGLP ...String:
MTDIVLNDLP FVDGPPAEGQ SRISWIKNGE EILGADTQYG SEGSMNRPTV SVLRNVEVLD KNIGILKTSL ETANSDIKTI QGILDVSGD IEALAQIGIN KKDISDLKTL TSEHTEILNG TNNTVDSILA DIGPFNAEAN SVYRTIRNDL LWIKRELGQY T GQDINGLP VVGNPSSGMK HRIINNTDVI TSQGIRLSEL ETKFIESDVG SLTIEVGNLR EELGPKPPSF SQNVYSRLNE ID TKQTTVE SDISAIKTSI GYPGNNSIIT SVNTNTDNIA SINLELNQSG GIKQRLTVIE TSIGSDDIPS SIKGQIKDNT TSI ESLNGI VGENTSSGLR ANVSWLNQIV GTDSSGGQPS PPGSLLNRVS TIETSVSGLN NAVQNLQVEI GNNSAGIKGQ VVAL NTLVN GTNPNGSTVE ERGLTNSIKA NETNIASVTQ EVNTAKGNIS SLQGDVQALQ EAGYIPEAPR DGQAYVRKDG EWVFL STFL SPA

UniProtKB: Fibritin

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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 / Pretreatment - Type: GLOW DISCHARGE
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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