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- PDB-9oae: Composite reconstruction of the thermophilic bacteriophage P74-26... -

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Basic information

Entry
Database: PDB / ID: 9oae
TitleComposite reconstruction of the thermophilic bacteriophage P74-26 Neck and Portal Vertex
Components
  • (DNA (31-MER)) x 2
  • (DNA (66-MER)) x 2
  • Adaptor (P74p90)
  • Collar (P74p112)
  • Major head protein
  • P74-26 Head Decoration Protein
  • Portal Vertex Protein
  • Portal protein
  • Tail Tube Protein gp93
  • Tail terminator
KeywordsVIRUS/DNA / bacteriophage / thermophilic / Neck / Portal / VIRUS / VIRUS-DNA complex
Function / homology
Function and homology information


host cell cytoplasm
Similarity search - Function
Phage tail tube protein-like / Phage tail tube protein / : / Phage P23-45 portal protein / Major capsid protein GpE / Phage major capsid protein E
Similarity search - Domain/homology
DNA / DNA (> 10) / Uncharacterized protein / Portal protein / Uncharacterized protein / Major head protein / Uncharacterized protein / Tail terminator / Major capsid protein / Uncharacterized protein
Similarity search - Component
Biological speciesOshimavirus P7426
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSedivy, E.L. / Agnello, E. / Song, K. / Xu, C. / Kelch, B.A.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Aa: Major head protein
Ab: Major head protein
Ac: Major head protein
Ad: Major head protein
Ae: Major head protein
Af: Major head protein
Ag: Major head protein
Ah: Major head protein
Ai: Major head protein
Aj: Major head protein
Ak: Major head protein
Al: Major head protein
Am: Major head protein
An: Major head protein
Ao: Major head protein
Ap: Major head protein
Aq: Major head protein
Ar: Major head protein
As: Major head protein
At: Major head protein
Ba: P74-26 Head Decoration Protein
Bb: P74-26 Head Decoration Protein
Bc: P74-26 Head Decoration Protein
Bd: P74-26 Head Decoration Protein
Be: P74-26 Head Decoration Protein
Bf: P74-26 Head Decoration Protein
Bg: P74-26 Head Decoration Protein
Bh: P74-26 Head Decoration Protein
Bi: P74-26 Head Decoration Protein
Bj: P74-26 Head Decoration Protein
Bk: P74-26 Head Decoration Protein
Bl: P74-26 Head Decoration Protein
Bm: P74-26 Head Decoration Protein
Bn: P74-26 Head Decoration Protein
Bo: P74-26 Head Decoration Protein
Bp: P74-26 Head Decoration Protein
Bq: P74-26 Head Decoration Protein
Br: P74-26 Head Decoration Protein
Bs: P74-26 Head Decoration Protein
Bt: P74-26 Head Decoration Protein
Ca: Portal Vertex Protein
Cb: Portal Vertex Protein
Cc: Portal Vertex Protein
Cd: Portal Vertex Protein
Ce: Portal Vertex Protein
Da: Portal protein
Db: Portal protein
Dc: Portal protein
Dd: Portal protein
De: Portal protein
Df: Portal protein
Dg: Portal protein
Dh: Portal protein
Di: Portal protein
Dj: Portal protein
Dk: Portal protein
Dl: Portal protein
Ea: Adaptor (P74p90)
Eb: Adaptor (P74p90)
Ec: Adaptor (P74p90)
Ed: Adaptor (P74p90)
Ee: Adaptor (P74p90)
Ef: Adaptor (P74p90)
Eg: Adaptor (P74p90)
Eh: Adaptor (P74p90)
Ei: Adaptor (P74p90)
Ej: Adaptor (P74p90)
Ek: Adaptor (P74p90)
El: Adaptor (P74p90)
Fa: Tail terminator
Fb: Tail terminator
Fc: Tail terminator
Fd: Tail terminator
Fe: Tail terminator
Ff: Tail terminator
Ga: Collar (P74p112)
Gb: Collar (P74p112)
Gc: Collar (P74p112)
Gd: Collar (P74p112)
Ge: Collar (P74p112)
Gf: Collar (P74p112)
Gg: Collar (P74p112)
Gh: Collar (P74p112)
Gi: Collar (P74p112)
Gj: Collar (P74p112)
Gk: Collar (P74p112)
Gl: Collar (P74p112)
Ha: Collar (P74p112)
Hb: Collar (P74p112)
Hc: Collar (P74p112)
Hd: Collar (P74p112)
He: Collar (P74p112)
Hf: Collar (P74p112)
Hg: Collar (P74p112)
Hh: Collar (P74p112)
Hi: Collar (P74p112)
Hj: Collar (P74p112)
Hk: Collar (P74p112)
Hl: Collar (P74p112)
Ia: Tail Tube Protein gp93
Ib: Tail Tube Protein gp93
Ic: Tail Tube Protein gp93
Id: Tail Tube Protein gp93
Ie: Tail Tube Protein gp93
If: Tail Tube Protein gp93
Ja: DNA (31-MER)
Jb: DNA (31-MER)
Jc: DNA (31-MER)
Jd: DNA (31-MER)
Je: DNA (31-MER)
Jf: DNA (31-MER)
Jg: DNA (31-MER)
Jh: DNA (31-MER)
Ji: DNA (31-MER)
Jj: DNA (31-MER)
Ka: DNA (66-MER)
Kb: DNA (66-MER)


Theoretical massNumber of molelcules
Total (without water)2,894,272117
Polymers2,894,272117
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 8 types, 105 molecules AaAbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtBaBbBcBdBeBfBgBhBiBj...

#1: Protein
Major head protein


Mass: 46680.754 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXR6
#2: Protein
P74-26 Head Decoration Protein


Mass: 16376.630 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXR5
#3: Protein
Portal Vertex Protein


Mass: 8431.445 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXK1
#4: Protein
Portal protein


Mass: 46634.465 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXR3
#5: Protein
Adaptor (P74p90)


Mass: 14556.551 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXR8
#6: Protein
Tail terminator


Mass: 17584.779 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXS1
#7: Protein ...
Collar (P74p112)


Mass: 16145.413 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXU5
#8: Protein
Tail Tube Protein gp93


Mass: 37955.738 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXS2

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DNA chain , 4 types, 12 molecules JaJcJeJgJiJbJdJfJhJjKaKb

#9: DNA chain
DNA (31-MER)


Mass: 9385.020 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426
#10: DNA chain
DNA (31-MER)


Mass: 9664.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426
#11: DNA chain DNA (66-MER)


Mass: 20091.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426
#12: DNA chain DNA (66-MER)


Mass: 20603.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Oshimavirus P7426VIRUSall0NATURAL
2Portal vertexCOMPLEX#1-#31NATURAL
3NeckCOMPLEX#4-#121NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Oshimavirus P7426466052
32Oshimavirus P7426466052
43Oshimavirus P7426466052
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Thermus thermophilus HB8 / Strain: HB8
Virus shellName: capsid / Diameter: 820 nm / Triangulation number (T number): 7
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Virions were purified from infected Thermus thermophilus using cesium chloride and sucrose gradient ultracentrifugation
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.0571 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16184

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Processing

EM software
IDNameVersionCategoryDetails
1UCSF ChimeraXparticle selectionused to merge maps into composite
2PHENIX1.21.2_5419model refinement
13UCSF ChimeraX3D reconstructionused to merge maps into composite
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90827 / Algorithm: FOURIER SPACE
Details: Number of particles used represents the sum of the number of particles in each of the independent maps combined to make this composite. Resolution represents the average resolution of the ...Details: Number of particles used represents the sum of the number of particles in each of the independent maps combined to make this composite. Resolution represents the average resolution of the three independent maps combined to make this composite
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 213.69 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0042178866
ELECTRON MICROSCOPYf_angle_d0.5868245412
ELECTRON MICROSCOPYf_chiral_restr0.046727049
ELECTRON MICROSCOPYf_plane_restr0.005430544
ELECTRON MICROSCOPYf_dihedral_angle_d14.55327951

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