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- EMDB-65386: Core proteins of the bacteriophage E1004 -

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Basic information

Entry
Database: EMDB / ID: EMD-65386
TitleCore proteins of the bacteriophage E1004
Map data
Sample
  • Virus: Escherichia phage (virus)
    • Protein or peptide: Gp17
    • Protein or peptide: Gp28
    • Protein or peptide: Gp27
    • Protein or peptide: Gp29
KeywordsComplex / VIRAL PROTEIN
Biological speciesEscherichia phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 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_65386.png

Downloads & links

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Map

FileDownload / File: emd_65386.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 344 pix.
= 378.4 Å		1.1 Å/pix.
x 344 pix.
= 378.4 Å		1.1 Å/pix.
x 344 pix.
= 378.4 Å

Surface

Projections

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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-0.9451069 - 1.4783264
Average (Standard dev.)0.006909124 (±0.0647664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 378.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65386_msk_1.map
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Half map: #2

Fileemd_65386_half_map_1.map
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Half map: #1

Fileemd_65386_half_map_2.map
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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: Gp17
    • Protein or peptide: Gp28
    • Protein or peptide: Gp27
    • Protein or peptide: Gp29

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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: Gp17

MacromoleculeName: Gp17 / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 7.814832 KDa
SequenceString:
MCFSPKISTP KPSVQAPEPA PLSEEVASVD IGAESDVDTN ETKGIKDLKV KKESAPKDKS SVSRAMRNSG VNMG

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Macromolecule #2: Gp28

MacromoleculeName: Gp28 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 85.34275 KDa
SequenceString: MASNIESALA NRTMGRGRAP GKTIAVNYQA ASVQAPTGDS GLARALTSFV ESGTGLYKQF KDEEKTRADE RSNEIIRKLT PQQRREAIQ NGTLLYQDDP YAMEALRVKT GRNAAFAVDD EINVKIQNGE FRTRQDMEEY RHQRLQDAAK SYAEEAGINP T DEFFQRGF ...String:
MASNIESALA NRTMGRGRAP GKTIAVNYQA ASVQAPTGDS GLARALTSFV ESGTGLYKQF KDEEKTRADE RSNEIIRKLT PQQRREAIQ NGTLLYQDDP YAMEALRVKT GRNAAFAVDD EINVKIQNGE FRTRQDMEEY RHQRLQDAAK SYAEEAGINP T DEFFQRGF NDNITDRNIA IYGSFNKYFS KQSEETAMLN TRIEMNSFLN DGDLMRSPES GKTFMAYLRD GLTTAAIPSD QR AREVITQ TVRDAIQKSG GSNFLQQVRG ERITLNGVDA TVEEIVGPDV FNAAIVEAQG TEYKLVAKYQ EDLALGVQSA ILQ DDPTIG LAQIQKLKEQ NNLLQPGEEL TPQRQMLINA EASLLEAVKR KSAEQAKENT KLIQTQNKQL VIDQVYQRRL AGDN VSTNY EDLPVSEATG EFKRSDMNNY ASAKLQQIDQ MDIPEAAKDA QKVALLRADT NNGPFRNAFQ TLTQDAAGEW QAAVI RGQY DPDKMQRFES LRRAYTQDPS SFAALYPDQA QLFSTFDQMD KIGLDPQTMI EADKQAASQS REMRMESDKA WQELKN DSR NKDLSRLPTS LDASARKVWD SWYYRTGNAD AATQQTQRWL NENTVTFQSE GSDGKSIGMV SKHQLMVGDN PESWQVG RD IIDTARKQLI KANPWVVNSQ LSVVEQNGSI FLQDATGTIR IRYDKELVGK LYREQQQKAQ DAAYAQAERD ANKRARIV G TKAAGDKRRA DREANIEKRG GMYNDVSLEG IAKVLIGKE

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Macromolecule #3: Gp27

MacromoleculeName: Gp27 / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 20.326736 KDa
SequenceString: MCEPVSIGLG IMSVAGATMS ASQQAKAEGA AIDAQNRQAQ EMIKQMNYSD ANLKMQERDL KEQQMAELTE TTLNGIRNQG MVRAAVAES GLEGNSMDRI ERQVAGDTVK ERAGITESYN RDYAAIFGNR IANIENTQSA IRGQGKIIKT SPLAHALNVA T AGVQGYAA ...String:
MCEPVSIGLG IMSVAGATMS ASQQAKAEGA AIDAQNRQAQ EMIKQMNYSD ANLKMQERDL KEQQMAELTE TTLNGIRNQG MVRAAVAES GLEGNSMDRI ERQVAGDTVK ERAGITESYN RDYAAIFGNR IANIENTQSA IRGQGKIIKT SPLAHALNVA T AGVQGYAA GKSMSGTSGS GGAAPISAAK GTPTGHS

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Macromolecule #4: Gp29

MacromoleculeName: Gp29 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage (virus)
Molecular weightTheoretical: 141.116766 KDa
SequenceString: MATRGIRNNN PGNIRVSKDQ WEGMTGDDGA FVTFDSPESG VRALGKNLLS YGRQGYDSIE KIINRWAPPN ENDTKAYIDS VVAATGIPA TQSLDLSNQD TLSALAQAIS FHETGSRYDP EVYQKGVARA LNGISPKTPP VSANVFDALT EGLKAKPKVA L GENLPTAA ...String:
MATRGIRNNN PGNIRVSKDQ WEGMTGDDGA FVTFDSPESG VRALGKNLLS YGRQGYDSIE KIINRWAPPN ENDTKAYIDS VVAATGIPA TQSLDLSNQD TLSALAQAIS FHETGSRYDP EVYQKGVARA LNGISPKTPP VSANVFDALT EGLKAKPKVA L GENLPTAA GLNIEGQAPE APNESFGEMF YKSTGETMQE REDRSTWFGF GAATEAEVKN SMVGVAIRAG QTEDSLDVIG DV FNPTRWN NHKWTREELD QIRNAGVLPQ YYGVITGGSP QNLTELINLA LENQKLDQEK AKAGTGAQLA AGVIGAGVDP LTY VPIAGQ VGKGGKLVNK MFTVAAQSGA LAGVSEMART SVAGGDAHVA EAILGGALFG GGMTAIADGL GRALGRNTNE FAGP ATRLE ARETARNVDG QDLSRLPIQE GEQTFSHQGV KFADVPNEPG SVRLEDGSIL IGENPLNPKT RQVFDEVIEP ERAAA GVNL GGLTEIGLKL LRSENPEIRG VAADLVRSPT GMQSGASGKI GTTASDVFER LRAVDHRFYN DIDDAVTEAL KDPYFQ TAF WRDSGAFRQD IYQRVSMAIE DGSGNLKAEL TPGELKVYDL LKNQFDAKRE MMENPAMFGR PDAQSIFPGS RFKGTYV PH VYSSQMKELY IKELGSPEAL QEAIKKSWLT SYASRPEVKK RVDEALLEAD PTLTPEGLAA AVDKYANDKA YGISHTEQ F ERSSVMEENI NGLVGLENNS FLEARNLFDS DMSIVLPNGQ TFSVNNLREW DMDKIVPAYN RRVNGDIAIM AGTGKTTKE MKDLVETLMN KAGDDGKLKG EVSTLRDTLK ILTGRARRDG ADDAAFATVM RTMTDLAFFA KNAYMGVQNL TEIGGMLARG NVRAMLHGV PMFRDLAFRN KKVGASEIKD LHNVIFGKEL DDSIRPSKQD VIDRLRSYSD LGRGAATALG TAKYYTGELA V RSPFTKVL NGTTNYLLDA GRQGFLSDIV EHSLTGSKRR FDDRWLKTAG ISDEQWKGIK SLIRESVTRG PDGKYTIKDK KA FSQDQRA MDLWRMGDTI ADETLLRPHK LSNMDAKAYG PIAKTVLQFK NFVIKSINGR TMRTFYNATK NNRAMDAALS TVM SMGLAG MYYMAQAHIK AYAMQDGRDR EYLKQALNPT MIGYAALSRS SHLGGPLGVA NILGGIAGYE DTKMLRSSIL PRSP TEKTE KPIAFGAASS GPVMNVVGNF LEQVPAFGYA ANVGATAYNL AGYLKADTRV NERDYMTGMY NTFRELVPND PITQK LLLG TFEEQGIHIK D

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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: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 32932
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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