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- EMDB-70879: Penton focused D3 virion capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-70879
TitlePenton focused D3 virion capsid
Map data
Sample
  • Virus: Pseudomonas phage D3 (virus)
KeywordsC5 symmetry / bacteriophage / capsid / HK97 fold / Virus
Biological speciesPseudomonas phage D3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBelford AK / Huet A / Maurer JB / Duda RL / Conway JF
Funding support United States, 2 items
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, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70879.png

Downloads & links

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Map

FileDownload / File: emd_70879.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å		0.82 Å/pix.
x 600 pix.
= 492. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.0442713 - 0.08284694
Average (Standard dev.)0.00007632805 (±0.0030318492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 492.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70879_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70879_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage D3

EntireName: Pseudomonas phage D3 (virus)
Components
  • Virus: Pseudomonas phage D3 (virus)

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Supramolecule #1: Pseudomonas phage D3

SupramoleculeName: Pseudomonas phage D3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2932880 / Sci species name: Pseudomonas phage D3 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 40 MDa
Virus shellShell ID: 1 / Name: virion capsid / Diameter: 750.0 Å / T number (triangulation number): 9

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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

Concentration30 mg/mL
BufferpH: 6
Component:
ConcentrationName
50.0 mMTRIS
50.0 mMBis TRIS
100.0 mMPotassium glutamate
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 43546 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 320746
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2ft1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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