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

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Basic information

Entry
Database: PDB / ID: 9oab
TitleC3 reconstruction of the thermophilic bacteriophage P74-26 Neck
Components
  • Adaptor (P74p90)
  • Collar (P74p112)
  • Portal protein
  • Tail Tube Protein gp93
  • Tail terminator
KeywordsVIRUS / bacteriophage / thermophilic / Neck / Portal
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 28, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / 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: Mask / Part number: 1 / Data content type: Mask / 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
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


Theoretical massNumber of molelcules
Total (without water)1,492,18660
Polymers1,492,18660
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Portal protein


Mass: 49731.172 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Oshimavirus P7426 / References: UniProt: A7XXR3
#2: 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
#3: 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
#4: 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
#5: 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
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
IDNameTypeDetailsEntity IDParent-IDSource
1Oshimavirus P7426VIRUSVirions were purified from infected Thermus thermophilus using cesium chloride gradient ultracentrifugation.all0NATURAL
2NeckCOMPLEXall1NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Oshimavirus P7426466052
32Oshimavirus P7426466052
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NONOSPECIESVIRION
22
Natural host
IDEntity assembly-IDOrganismNcbi tax-IDStrain
11Thermus thermophilus HB8300852HB8
22Thermus thermophilus HB8300852
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 gradient ultracentrifugation.
Specimen supportGrid material: COPPER / 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
IDNameVersionCategory
7Cootmodel fitting
8ISOLDEmodel fitting
9UCSF ChimeraXmodel fitting
11PHENIXdev_5430model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30748 / Algorithm: FOURIER SPACE
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.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Initial model was created by ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 75.95 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023102336
ELECTRON MICROSCOPYf_angle_d0.5134139212
ELECTRON MICROSCOPYf_chiral_restr0.043515576
ELECTRON MICROSCOPYf_plane_restr0.00518216
ELECTRON MICROSCOPYf_dihedral_angle_d4.192613950

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