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- EMDB-43793: phi29 empty capsid maturation intermediate with wild-type pRNA -

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Basic information

Entry
Database: EMDB / ID: EMD-43793
Titlephi29 empty capsid maturation intermediate with wild-type pRNA
Map dataempty phi29 capsid maturation intermediate
Sample
  • Virus: Bacillus phage phi29 (virus)
Keywordsbacteriophage / prohead / HK97 fold / VIRUS
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWoodson ME / Morais MC / Zhang W / Jardine PJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122979 United States
CitationJournal: Sci Adv / Year: 2025
Title: Phi29 assembly intermediates reveal how scaffold interactions with capsid protein drive capsid construction and maturation.
Authors: Michael Woodson / Nikolai S Prokhorov / Seth D Scott / Wei Zhao / Wei Zhang / Kyung H Choi / Paul J Jardine / Marc C Morais /
Abstract: The self-assembly of bacteriophage capsids from major capsid proteins (MCPs) and scaffolding proteins (SPs) and the subsequent expansion of these capsids are essential steps in bacteriophage life ...The self-assembly of bacteriophage capsids from major capsid proteins (MCPs) and scaffolding proteins (SPs) and the subsequent expansion of these capsids are essential steps in bacteriophage life cycles. However, the mechanism by which assembly occurs remains poorly understood, and few intermediate states are available to illuminate the expansion of meta-stable procapsids into robust mature capsids. Here, we present the structure of a partially expanded phi29 procapsid that reveals distinct conformations of MCPs and allows visualization of SPs in multiple oligomeric states. These results suggest that formation of SP dimers, tetramers, and higher-order oligomers drives dissociation of SP from MCP to actuate capsid expansion. Hexons expand first, and we propose penton maturation is delayed by a symmetry match with SP oligomers. We further show that the prolate shape of phi29's capsid is possible due to concave hexons in the equatorial region of the capsid that may alter interactions with SP and explain the observed dependence of the prolate shape on SP.
History
DepositionFeb 23, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43793.png

Downloads & links

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Map

FileDownload / File: emd_43793.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationempty phi29 capsid maturation intermediate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 704 pix.
= 957.44 Å		1.36 Å/pix.
x 704 pix.
= 957.44 Å		1.36 Å/pix.
x 704 pix.
= 957.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0486
Minimum - Maximum-0.10194965 - 0.20397209
Average (Standard dev.)0.0006371663 (±0.006752216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions704704704
Spacing704704704
CellA=B=C: 957.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: empty phi29 capsid maturation intermediate even half map

Fileemd_43793_half_map_1.map
Annotationempty phi29 capsid maturation intermediate even half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: empty phi29 capsid maturation intermediate odd half map

Fileemd_43793_half_map_2.map
Annotationempty phi29 capsid maturation intermediate odd half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacillus phage phi29

EntireName: Bacillus phage phi29 (virus)
Components
  • Virus: Bacillus phage phi29 (virus)

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Supramolecule #1: Bacillus phage phi29

SupramoleculeName: Bacillus phage phi29 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2884424 / Sci species name: Bacillus phage phi29 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Bacillus subtilis (bacteria)
Virus shellShell ID: 1 / Name: capsid / Diameter: 35.0 Å / T number (triangulation number): 3

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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: 7.8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
5.0 mMMgCl2magnesium chloride
50.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1401 / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 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

Particle selectionNumber selected: 27185
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: EMD-6560
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 15892
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 15892 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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