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- EMDB-64113: Phage T4 hub in post-tail contraction, pre-genome-release state -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64113
TitlePhage T4 hub in post-tail contraction, pre-genome-release state
Map data
Sample
  • Virus: Escherichia phage T4 (virus)
    • Protein or peptide: Tail tube protein gp19
    • Protein or peptide: Baseplate tail-tube junction protein gp54
    • Protein or peptide: Baseplate tail-tube junction protein gp48
KeywordsBacteriophage / Myovirus / Phage T4 / tail contraction / phage hub complex / tape-measure protein / genome release / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, tube / virus tail, baseplate / viral tail assembly / structural molecule activity
Similarity search - Function
Baseplate tail-tube protein gp48, T4-like virus / Tail-tube assembly protein / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19
Similarity search - Domain/homology
Tail tube protein gp19 / Baseplate tail-tube junction protein gp48 / Baseplate tail-tube junction protein gp54
Similarity search - Component
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShao Q / Dong J / Wang A / Li L / Zheng Y / Li H / Li Y / Zhang Q / Sun L / Fokine A ...Shao Q / Dong J / Wang A / Li L / Zheng Y / Li H / Li Y / Zhang Q / 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: To Be Published
Title: Near-atomic structure of a viral genome delivery machine intermediate from bacteriophage T4
Authors: Shao Q / Dong J / Wang A / Li L / Zheng Y / Li H / Li Y / Zhang Q / Sun L / Fokine A / Rao VB / Tao P / Fang Q
History
DepositionApr 10, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64113.png

Downloads & links

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Map

FileDownload / File: emd_64113.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 240 pix.
= 393.12 Å		1.64 Å/pix.
x 240 pix.
= 393.12 Å		1.64 Å/pix.
x 240 pix.
= 393.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0143
Minimum - Maximum-0.06223873 - 0.12453752
Average (Standard dev.)0.000097969416 (±0.0046819956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 393.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64113_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64113_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64113_half_map_2.map
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: Tail tube protein gp19
    • Protein or peptide: Baseplate tail-tube junction protein gp54
    • Protein or peptide: Baseplate tail-tube junction protein gp48

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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 tube protein gp19

MacromoleculeName: Tail tube protein gp19 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: Baseplate tail-tube junction protein gp54

MacromoleculeName: Baseplate tail-tube junction protein gp54 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 35.015234 KDa
SequenceString: MYSLEEFNNQ AINADFQRNN MFSCVFATTP STKSSSLISS ISNFSYNNLG LNSDWLGLTQ GDINQGITTL ITAGTQKLIR KSGVSKYLI GAMSQRTVQS LLGSFTVGTY LIDFFNMAYN SSGLMIYSVK MPENRLSYET DWNYNSPNIR ITGRELDPLV I SFRMDSEA ...String:
MYSLEEFNNQ AINADFQRNN MFSCVFATTP STKSSSLISS ISNFSYNNLG LNSDWLGLTQ GDINQGITTL ITAGTQKLIR KSGVSKYLI GAMSQRTVQS LLGSFTVGTY LIDFFNMAYN SSGLMIYSVK MPENRLSYET DWNYNSPNIR ITGRELDPLV I SFRMDSEA CNYRAMQDWV NSVQDPVTGL RALPQDVEAD IQVNLHSRNG LPHTAVMFTG CIPISVSAPE LSYDGDNQIT TF DVTFAYR VMQAGAVDRQ RALEWLESAA INGIQSVLGN SGGVTGLSNS LSRLSRLGGT AGSISNINTM TGIVNSQSKI LGA I

UniProtKB: Baseplate tail-tube junction protein gp54

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Macromolecule #3: Baseplate tail-tube junction protein gp48

MacromoleculeName: Baseplate tail-tube junction protein gp48 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 39.770332 KDa
SequenceString: MAIVKEITAD LIKKSGEKIS AGQSTKSEVG TKTYTAQFPT GRASGNDTTE DFQVTDLYKN GLLFTAYNMS SRDSGSLRSM RSNYSSSSS SILRTARNTI SSTVSKLSNG LISNNNSGTI SKSPIANILL PRSKSDVDTS SHRFNDVQES LISRGGGTAT G VLSNIAST ...String:
MAIVKEITAD LIKKSGEKIS AGQSTKSEVG TKTYTAQFPT GRASGNDTTE DFQVTDLYKN GLLFTAYNMS SRDSGSLRSM RSNYSSSSS SILRTARNTI SSTVSKLSNG LISNNNSGTI SKSPIANILL PRSKSDVDTS SHRFNDVQES LISRGGGTAT G VLSNIAST AVFGALESIT QGIMADNNEQ IYTTARSMYG GAENRTKVFT WDLTPRSTED LMAIINIYQY FNYFSYGETG KS QYAAEIK GYLDDWYRST LIEPLSPEDA AKNKTLFEKM TSSLTNVLVV SNPTVWMVKN FGATSKFDGK TEIFGPCQIQ SIR FDKTPN GNFNGLAIAP NLPSTFTLEI TMREIITLNR ASLYAGTF

UniProtKB: Baseplate tail-tube junction protein gp48

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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 / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
SoftwareName: EPU
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: 0.25 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: 0.25 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: 40108
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 36951
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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