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- EMDB-65388: Structure of the bacteriophage E1004 tail -

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Basic information

Entry
Database: EMDB / ID: EMD-65388
TitleStructure of the bacteriophage E1004 tail
Map data
Sample
  • Virus: Escherichia phage (virus)
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Nozzle protein
    • Protein or peptide: Adaptor protein
KeywordsComplex / VIRAL PROTEIN
Biological speciesEscherichia phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsSun BN / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: Structure / Year: 2025
Title: Cryo-EM structure of drug-resistant Escherichia coli phage E1004 reveals a conserved cylindrical core among podophages.
Authors: Binning Sun / Jing Zheng / Yuan Fu / Fengyuan Tian / Hao Xiao / Su Li / Lingpeng Cheng / Ping Chen / Hongrong Liu /
Abstract: Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution ...Podophage tails are too short to traverse the cell envelope and require internal core proteins to assemble into a transmembrane channel for genome delivery during infection. However, high-resolution structures of near-complete cores remain scarce. Here, we present the near-atomic-resolution cryo-electron microscopy (cryo-EM) structure of the drug-resistant E. coli phage E1004, which features a T7-like core-portal-tail structure with six P22-like tailspikes. We found that the cylindrical core comprises four proteins: gp17, gp27, gp28, and gp29. Gp29 forms a tetramer, while gp28 and gp27 assemble into octamers. Notably, there are sixteen copies of gp17 in two conformations, distinct from the small core protein gp6.7 in T7. The gp17-gp27 complex reveals the mechanism for mediating the symmetry adjustment at the core-portal interface. Moreover, comparative analysis with other podophage cores highlights diversity in core protein composition and organization, particularly among the small core proteins. We propose that these variations represent evolutionary adaptations to diverse host envelopes.
History
DepositionJul 16, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65388.png

Downloads & links

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Map

FileDownload / File: emd_65388.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 440 pix.
= 484. Å		1.1 Å/pix.
x 440 pix.
= 484. Å		1.1 Å/pix.
x 440 pix.
= 484. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.77781636 - 1.4391816
Average (Standard dev.)0.0013482068 (±0.057010055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 484.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65388_msk_1.map
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Half map: #2

Fileemd_65388_half_map_1.map
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Half map: #1

Fileemd_65388_half_map_2.map
Projections & Slices
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Sample components

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Entire : Escherichia phage

EntireName: Escherichia phage (virus)
Components
  • Virus: Escherichia phage (virus)
    • Protein or peptide: Tail spike protein
    • Protein or peptide: Nozzle protein
    • Protein or peptide: Adaptor protein

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Supramolecule #1: Escherichia phage

SupramoleculeName: Escherichia phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 3102713 / Sci species name: Escherichia phage / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tail spike protein

MacromoleculeName: Tail spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 90.53382 KDa
SequenceString: MSTITQFPSG NTQYRIEFDY LARTFVVVTL VNSSNPTLNR VLEVGRDYRF LNPTMIEMLV DQSGFDIVRI HRQTGTDLVV DFRNGSVLT ASDLTNSELQ AIHIAEEGRD QTVDLAKEYA DAAGSSAGNA KDSEDEARRI AESIREAGLI GYITRRSFEK G YNVTTWSE ...String:
MSTITQFPSG NTQYRIEFDY LARTFVVVTL VNSSNPTLNR VLEVGRDYRF LNPTMIEMLV DQSGFDIVRI HRQTGTDLVV DFRNGSVLT ASDLTNSELQ AIHIAEEGRD QTVDLAKEYA DAAGSSAGNA KDSEDEARRI AESIREAGLI GYITRRSFEK G YNVTTWSE VLLWEEDGDY YRWDGTLPKN VPAGSTPETS GGIGLGAWVS VGDAALRSQI SNPEGAILYP ELQMARWRDE GD VRGWGAK GDGVTDSTEN IAASLNSQKA VVASEGVFSS SGINSNYCNL DGRGSGVLSH RSSTGNYLVF NNPRTGRLSN ITV ESNKAT DTTQGQQVSL AGGSDVTVSD VNFSNVKGTG FSLIAYPNDV PPDGLMIKGI RGSYSGYATN KAAGCVLADS SVNS LIDNV IAKNYPQFGA VELKGTASYN IVSNVIGTDC QHVTYNGTKG SIAPSNNLIK GVVANNPKYA AVVAGKGSTN LISDV LVDY STSDARQAHG VTVEGSDNVI NNVLMTGCDG TNSLGQAQTA TITRFIDTAN NNYASVFPSY SATGVITFES GSTRNF VEV KHPGRRNDLL SATGTISGAD TIDGTDNSNV VHAPALGQYI GSMSGRFEWR IKSMSLPSGV LTSADKYRML ADGAVSL AV GGGTSSQVRL FTSDGTYRNI SLTSGNVRLP TSSTGYLQLG SNAMTPDSTN TYALGSASRA WSGGFTQSAF TVVSDARD K TEPLNISDAL LDAWSEVDFV QFQYLGRIEE KGADSARWHF GIIAQRAKEA FERHGIDAHR YGFLCFDSWD DVYEEDANG SRKLITPAGS RYGIRYEEVL ILEAALMRRT IKRMQEALAV MSK

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Macromolecule #2: Nozzle protein

MacromoleculeName: Nozzle protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 86.595641 KDa
SequenceString: MPLITQSIKN LKGGISQQPD ILRFSDQGES QVNCWSSESD GLQKRPPTVF KRRLNIDVES NPKFHLINRD EHEQYYIVFN GSNIQVVDL SGNQYSVSGA VEYVTSSNPR DDIRVVTVAD YTFVVNRKVV VKGGSEKSHP GYNRKARALI NLRGGQYGRT L KVGINGGV ...String:
MPLITQSIKN LKGGISQQPD ILRFSDQGES QVNCWSSESD GLQKRPPTVF KRRLNIDVES NPKFHLINRD EHEQYYIVFN GSNIQVVDL SGNQYSVSGA VEYVTSSNPR DDIRVVTVAD YTFVVNRKVV VKGGSEKSHP GYNRKARALI NLRGGQYGRT L KVGINGGV KVSHKLPAGN DAENDPPKVD AQAIGAAMRD LLVQAYPDFT FDLGSGFLLI TAPSGTDINS VETEDGYANQ LI SPVLDTV QTISKLPLAA PNGYIIKIQG ETNSSADEYY VMYDSNTKTW KETVEPGVIT GFDVTTMPHA LIRQSDGSFE FKT LDWSKR GSGNDDTNPM PSFVDATIND VFFYRNRLGF LSGENVIMSR SASYFAFFPK SVATLSDADP IDVAVSHPRI SILK YAVPF SEQLLLWSDE VQFVMTSSGV LTSKSIQLDV GSEFALGDTA RPFAVGRSVF FSAPRGSFTS IKRYFAVADV SDVKD ADDT TGHVLSYIPN GVFDIQGTGT ENYICVNSTG AYNRIYIYKF LFKDGVQLQA SWSHWEFPKD DKILASASIG STMFIV RQH QGGVDIEHLK FIKEATDFPS EPYRLHIDSK VSMVIPIGSY NADTYKTTVD IGAAYGGNAP SPGRYYLIDS QGAYVDL GD LTSISTVITL NGDWSGRTVF IGRPYLMSYK FSRFLIKIED DSGTQSEDTG RLQLRRAWVN YKDTGALRLI VRNGEREF V NTFNGYTLGQ QTIGTTNIGD GQYRFAMNGN ALTTSLTLES NYPTPVSIVG CGWEASYAKK ARSV

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Macromolecule #3: Adaptor protein

MacromoleculeName: Adaptor protein / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 21.456961 KDa
SequenceString:
MAQYIPLNAN DDLDAINDML AAIGEPAVLQ LDEGNADVSN AQRILHRVNR QVQAKGWNFN INEAAVLTPD VQDNRIRFLP SYLRVMTAG ATSYYSNMGG YLYDLSTQST TFTDPITVEL VEMKPFSEMP VVFRDYIVTK ASREFNAKFF GSPESELYLR E QEAELYQQ VMEYEMDTGR YNMMSDIGRD

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 µm
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50105
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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