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- PDB-9ouz: Icosahedral D3 expanded capsid -

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Basic information

Entry
Database: PDB / ID: 9ouz
TitleIcosahedral D3 expanded capsid
ComponentsMajor capsid protein
KeywordsVIRUS / C5 symmetry / bacteriophage / capsid / HK97 fold
Function / homology: / Phage capsid / Phage capsid family / virion component / Major capsid protein
Function and homology information
Biological speciesPseudomonas phage D3 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBelford, A.K. / Huet, A. / Maurer, J.B. / Duda, R.L. / Conway, J.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144981 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD025009 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into scaffold-guided assembly of the Pseudomonas phage D3 capsid.
Authors: Anna K Belford / Joshua B Maurer / Robert L Duda / Alexis Huet / James F Conway /
Abstract: Tailed bacteriophages comprise the largest structural family of viruses with close relatives in archaea and the eukaryotic herpesviruses. The common assembly pathway produces an icosahedrally ...Tailed bacteriophages comprise the largest structural family of viruses with close relatives in archaea and the eukaryotic herpesviruses. The common assembly pathway produces an icosahedrally symmetric protein shell, called capsid, into which the double-stranded DNA genome is packaged. While capsid sizes and amino acid sequences vary considerably, the major capsid protein (MCP) folds are remarkably similar throughout the family. To investigate the mechanisms governing capsid size, we characterize the procapsid and mature capsid of phage D3, which expresses an icosahedral lattice with Triangulation number T = 9. We find that the MCP scaffold domain binds to the interior capsid surface, acting as a clamp to constrain subunit interactions. Following scaffold digestion, the MCP capsid domains form strong interactions that maintain capsid structure throughout maturation. The scaffold constraints appear critical for capsid size determination and provide important understanding of the factors governing capsid assembly in general and expands our understanding of these ecologically and biomedically important viruses.
History
DepositionMay 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 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
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)385,8479
Polymers385,8479
Non-polymers00
Water00
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)23,150,840540
Polymers23,150,840540
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
x 5


  • icosahedral pentamer
  • 1.93 MDa, 45 polymers
Theoretical massNumber of molelcules
Total (without water)1,929,23745
Polymers1,929,23745
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.32 MDa, 54 polymers
Theoretical massNumber of molelcules
Total (without water)2,315,08454
Polymers2,315,08454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major capsid protein


Mass: 42871.926 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage D3 (virus) / References: UniProt: Q9XJT3
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

ComponentName: Pseudomonas phage D3 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 20 MDa / Experimental value: NO
Source (natural)Organism: Pseudomonas phage D3 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Pseudomonas aeruginosa
Virus shellName: expanded capsid / Diameter: 750 nm / Triangulation number (T number): 9
Buffer solutionpH: 6
Buffer component
IDConc.NameBuffer-ID
150 mMTRIS1
250 mMBis TRIS1
3100 mMPotassium glutamate1
SpecimenConc.: 30 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 298 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 / Calibrated magnification: 96000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 43546

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Processing

EM software
IDNameVersionCategory
1EMAN2particle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF ChimeraX1.9model fitting
9RELION4initial Euler assignment
10RELION4final Euler assignment
12RELION43D reconstruction
13ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1584 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 9OUS

9ous


Accession code: 9OUS / Source name: PDB / Type: experimental model

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