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- EMDB-70278: C3 reconstruction of the thermophilic bacteriophage P74-26 Neck -

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Basic information

Entry
Database: EMDB / ID: EMD-70278
TitleC3 reconstruction of the thermophilic bacteriophage P74-26 Neck
Map data
Sample
  • Virus: Oshimavirus P7426
    • Complex: Neck
      • Protein or peptide: Portal protein
      • Protein or peptide: Adaptor (P74p90)
      • Protein or peptide: Tail terminator
      • Protein or peptide: Collar (P74p112)
      • Protein or peptide: Tail Tube Protein gp93
Keywordsbacteriophage / thermophilic / Neck / Portal / VIRUS
Function / homologyPhage tail tube protein-like / Phage tail tube protein / : / Phage P23-45 portal protein / Portal protein / Uncharacterized protein / Tail terminator / Major capsid protein / Uncharacterized protein
Function and homology information
Biological speciesOshimavirus P7426
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSedivy EL / Agnello E / Song K / Xu C / Kelch BA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817338 United States
CitationJournal: J Mol Biol / Year: 2026
Title: The structure of a thermostable phage's portal vertex and neck complex illuminates the headful maturation mechanism.
Authors: Emma L Sedivy / Emily Agnello / Julia E Hobaugh / Rakeyah Ahsan / Kangkang Song / Chen Xu / Brian A Kelch /
Abstract: Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged ...Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged into its capsid shell through the portal complex. The portal complex then closes to retain DNA and connects to the tail, which is required for host recognition and infection. The trigger to stop pumping DNA and assemble the mature virus has been a longstanding conundrum in the field. We determined the structure of the portal, the proteins that connect it to the tail, and portal vertex in the hyperthermophilic phage Oshimavirus using cryo-Electron Microscopy (cryo-EM). We find highly intertwined loop structures, like in a wicker basket, potentially stabilizing the portal vertex against high temperatures. Moreover, we observe that the portal protrudes from the capsid in mature virions. We propose that portal is repositioned by packaged DNA, forming a pressure-sensitive switch that terminates genome packaging and triggers tail attachment in headful phages.
History
DepositionApr 21, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70278.png

Downloads & links

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Map

FileDownload / File: emd_70278.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.40161002 - 1.0243841
Average (Standard dev.)-0.003912003 (±0.057378497)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70278_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70278_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70278_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Oshimavirus P7426

EntireName: Oshimavirus P7426
Components
  • Virus: Oshimavirus P7426
    • Complex: Neck
      • Protein or peptide: Portal protein
      • Protein or peptide: Adaptor (P74p90)
      • Protein or peptide: Tail terminator
      • Protein or peptide: Collar (P74p112)
      • Protein or peptide: Tail Tube Protein gp93

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Supramolecule #1: Oshimavirus P7426

SupramoleculeName: Oshimavirus P7426 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Virions were purified from infected Thermus thermophilus using cesium chloride gradient ultracentrifugation.
NCBI-ID: 466052 / Sci species name: Oshimavirus P7426 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Thermus thermophilus HB8 (bacteria) / Strain: HB8
Virus shellShell ID: 1 / Name: capsid / Diameter: 820.0 Å / T number (triangulation number): 7

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Supramolecule #2: Neck

SupramoleculeName: Neck / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Oshimavirus P7426

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Macromolecule #1: Portal protein

MacromoleculeName: Portal protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 49.731172 KDa
SequenceString: MAKRGRKPKE LVPGPGSIDP SDVPKLEGAS VPVMSTSYDV VVDREFDELL QGKDGLLVYH KMLSDGTVKN ALNYIFGRIR SAKWYVEPA STDPEDIAIA AFIHAQLGID DASVGKYPFG RLFAIYENAY IYGMAAGEIV LTLGADGKLI LDKIVPIHPF N IDEVLYDE ...String:
MAKRGRKPKE LVPGPGSIDP SDVPKLEGAS VPVMSTSYDV VVDREFDELL QGKDGLLVYH KMLSDGTVKN ALNYIFGRIR SAKWYVEPA STDPEDIAIA AFIHAQLGID DASVGKYPFG RLFAIYENAY IYGMAAGEIV LTLGADGKLI LDKIVPIHPF N IDEVLYDE EGGPKALKLS GEVKGGSQFV SGLEIPIWKT VVFLHNDDGS FTGQSALRAA VPHWLAKRAL ILLINHGLER FM IGVPTLT IPKSVRQGTK QWEAAKEIVK NFVQKPRHGI ILPDDWKFDT VDLKSAMPDA IPYLTYHDAG IARALGIDFN TVQ LNMGVQ AINIGEFVSL TQQTIISLQR EFASAVNLYL IPKLVLPNWP SATRFPRLTF EMEERNDFSA AANLMGMLIN AVKD SEDIP TELKALIDAL PSKMRRALGV VDEVREAVRQ PADSRYLYTR RRR

UniProtKB: Portal protein

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Macromolecule #2: Adaptor (P74p90)

MacromoleculeName: Adaptor (P74p90) / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 14.556551 KDa
SequenceString:
MLPEVSVDEV WYYMPAEVRR PEEVVREGQG GVSLAAFRHI KNGVLAEAAS HLKANGVPEG LWNHELIRDY ILMQIAARIL RRVRAYQEL ADSLFADSNI KLRAFLEGVA QVAPDVGTGD WVEDEAILPP F

UniProtKB: Uncharacterized protein

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Macromolecule #3: Tail terminator

MacromoleculeName: Tail terminator / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 17.584779 KDa
SequenceString:
MNPDLKAAHH LKALLENFTW EYPDGEEGRF HQIDVGYFSR PSGYPYAAIH SAKSSAPVVR LGMGAGTLAR RFEIELVLTI EYEDPDPQR GYERLTTLRW EVFRHLVLNA QAIPGVEFTD LDEATIEAVT EDDGGFERWG FYGMVLIPIK VVLNPQ

UniProtKB: Tail terminator

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Macromolecule #4: Collar (P74p112)

MacromoleculeName: Collar (P74p112) / type: protein_or_peptide / ID: 4 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 16.145413 KDa
SequenceString:
MVIDYTITRG TLFVVPASGS VMEVFSPQDG FPLLKLRQEN GVFYLKPETT SLLAFSYGHY YVYDENRVLK QRGLLRVQGN LYAPANAQV ELLTFRGPGP HQVPALSGQP LLFVNGVLYQ DYQLADGVLQ VNGVQPEDEV VLVMLGG

UniProtKB: Uncharacterized protein

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Macromolecule #5: Tail Tube Protein gp93

MacromoleculeName: Tail Tube Protein gp93 / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Oshimavirus P7426
Molecular weightTheoretical: 37.955738 KDa
SequenceString: MRGVDTFLAF KEQADLKTPA TLASLAAGDF LAFNSESLSG RQQVIQSRAI RRMPMRQIAY TANGTVEAGG AVEFTTSNYV LKKLLPLIF HSKTGQEDDP DGDGATFTLV NGGVLTPFTA FVGFDGPEGK YVRRFFGAKV NQATFSARVN DMLNLNLDVQ A IGKDILQP ...String:
MRGVDTFLAF KEQADLKTPA TLASLAAGDF LAFNSESLSG RQQVIQSRAI RRMPMRQIAY TANGTVEAGG AVEFTTSNYV LKKLLPLIF HSKTGQEDDP DGDGATFTLV NGGVLTPFTA FVGFDGPEGK YVRRFFGAKV NQATFSARVN DMLNLNLDVQ A IGKDILQP GDPGWVNVTP VYPGGDEEYA YVFYQARVLI KAGDMADLAE LPVESFDLTI NHNLNTNRYR LGSIYRQSLD EG VTEVTGT FTLDAAVKSI SGPALNLTGG TAHDPAFLEK VALYGKYAAL KLEFIDPTRE VAEGVPCRLT IHLPFVRLEE PDF QVRDPG VITGSARFNA YETISVTHVA KF

UniProtKB: Major capsid 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: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV
DetailsVirions were purified from infected Thermus thermophilus using cesium chloride gradient ultracentrifugation.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 16184 / Average electron dose: 49.0571 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: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF
Details: FSC was calculated using the provided mask, which excludes the virus capsid and contents, because they do not have C3 symmetry and were not modeled here.
Number images used: 30748
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: Initial model was created by ModelAngelo
SoftwareName: Coot
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9oab:
C3 reconstruction of the thermophilic bacteriophage P74-26 Neck

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