Deposition

Crossed laser phase plate (xLPP) tomography of PP7 virus-like particles in E. coli: a matched-grid comparison with underfocus phase contrast

Deposition ID:CZCDP-10363

Release Date: 2026-09-11

Last Modified: 2026-09-11

key visualization for Crossed laser phase plate (xLPP) tomography of PP7 virus-like particles in E. coli: a matched-grid comparison with underfocus phase contrast

Photo Caption: Central slab of 4 representative tomograms with selected sets of annotations.

Deposition Overview

This deposition contains three cryoET datasets collected back-to-back on a single grid of Escherichia coli overexpressing PP7 virus-like particles (VLPs). The datasets compare conventional underfocus-based phase contrast with phase contrast generated by a crossed laser phase plate (xLPP): one xLPP-off dataset at 2-3 µm underfocus (67 tilt series collected), one xLPP-on dataset at 2-3 µm underfocus (68 tilt series collected), and one xLPP-on dataset at 0.5-1.5 µm underfocus (56 tilt series collected). Data is deposited with AreTomo3 baseline alignments and reconstructions and VLP particle positions and orientations. Subtomogram averaging of the PP7 VLPs yields reconstructions approaching the Nyquist limit in every dataset.

Authors

Deposition Data

Annotations:315

Tomograms:321

Publications

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Related Databases

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Methods Summary

Annotations	Method Type	Method Details	Method Links
26	Hybrid	Oriented PP7 VLP positions from RELION 5 subtomogram averaging with I2 symmetry, run with the py2rely STA pipeline. To balance the number of particles across three sessions, all 13,604 curated candidates on ice (the smallest set of the three sessions) were aligned to a PP7 VLP reference map at 9.6, 3.2, and 1.6 Å/px with repeated rounds of CTF refinement, Bayesian polishing, re-extraction and 3D auto-refinement. Deposited values are those of the particle set that gave the best map (3.5 Å at FSC 0.143), reached after 3D refinement after the fourth polishing round. Orientations are relative to the I2 reference and are defined up to the icosahedral symmetry. Averaging included two tomograms that are not part of this dataset, so 11,894 of the 13,211 refined particles are deposited. Two particles whose refined centre lies outside the reconstructed volume were omitted.	Source Code:copick +7 more
29	Hybrid	Oriented PP7 VLP positions from RELION 5 subtomogram averaging with I2 symmetry, run with the py2rely STA pipeline. To balance the number of particles across three sessions, a random subset of 13,604 of the 15,411 curated candidates on ice were selected and then aligned to a PP7 VLP reference map at 9.6, 3.2, and 1.6 Å/px with repeated rounds of CTF refinement, Bayesian polishing, re-extraction and 3D auto-refinement. Deposited values are those of the particle set that gave the best map (3.6 Å at FSC 0.143), reached after 3D refinement after the third polishing round. Orientations are relative to the I2 reference and are defined up to the icosahedral symmetry. Averaging included three tomograms that are not part of this dataset, so 13,093 of the 13,247 refined particles are deposited. Six particles whose refined centre lies outside the reconstructed volume were omitted.	Source Code:copick +7 more
49	Hybrid	Oriented PP7 VLP positions from RELION 5 subtomogram averaging with I2 symmetry, run with the py2rely STA pipeline. To balance the number of particles across three sessions, a random subset of 13,604 of the 17,322 curated candidates (see the curated annotation) were selected and then aligned to a PP7 VLP reference map at 9.6, 3.2, and 1.6 Å/px with repeated rounds of CTF refinement, Bayesian polishing, re-extraction and 3D auto-refinement. Deposited values are those of the particle set that gave the best map (3.4 Å at FSC 0.143), reached after the third polishing round. Orientations are relative to the I2 reference and are defined up to the icosahedral symmetry. Forty particles whose refined centre lies outside the reconstructed volume were omitted.	Source Code:copick +7 more
26	Hybrid	PP7 VLP candidates predicted with Octopi (3D U-Net segmentation with watershed localization) on DenoisET-denoised tomograms at 10 Å; 2D minislab projections of every candidate were extracted with slabpick, classified into 50 2D classes (and a second round of 25 classes) in RELION 5 via py2rely, classes showing intact VLPs were selected interactively and the retained candidates mapped back to the tomograms; subtomogram averaging started from this curated set (see the RELION-refined annotation).	Source Code:copick +7 more
78	Hybrid	PP7 VLP candidates predicted with Octopi (3D U-Net segmentation with watershed localization) on DenoisET-denoised tomograms at 10 Å; 2D minislab projections of every candidate were extracted with slabpick, classified into 50 2D classes in RELION 5 via py2rely, classes showing intact VLPs were selected interactively and the retained candidates mapped back to the tomograms; subtomogram averaging started from this curated set (see the RELION-refined annotation).	Source Code:copick +7 more
107	Automated	Automated PP7 VLP prediction with Octopi (3D U-Net segmentation with watershed localization) on DenoisET-denoised tomograms at 10 Å, before curation.	Source Code:copick +3 more

Deposited Data

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Data Contents

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FramesAvailable

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AlignmentAvailable

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315 of 315 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
102virus-like capsid Annotation ID: AN-184224	Point	Automated	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt741_ts_002
101virus-like capsid Annotation ID: AN-184223	Point	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt741_ts_002
100virus-like capsid Annotation ID: AN-184222	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt741_ts_002
102virus-like capsid Annotation ID: AN-184220	Point	Automated	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt740_ts_002
101virus-like capsid Annotation ID: AN-184219	Point	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt740_ts_002
100virus-like capsid Annotation ID: AN-184218	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt740_ts_002
102virus-like capsid Annotation ID: AN-184216	Point	Automated	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt739_ts_002
101virus-like capsid Annotation ID: AN-184215	Point	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt739_ts_002
100virus-like capsid Annotation ID: AN-184214	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt739_ts_002
102virus-like capsid Annotation ID: AN-184212	Point	Automated	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt738_ts_002
101virus-like capsid Annotation ID: AN-184211	Point	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt738_ts_002
100virus-like capsid Annotation ID: AN-184210	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt738_ts_002
102virus-like capsid Annotation ID: AN-184208	Point	Automated	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt737_ts_002
101virus-like capsid Annotation ID: AN-184207	Point	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt737_ts_002
100virus-like capsid Annotation ID: AN-184206	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt737_ts_002
102virus-like capsid Annotation ID: AN-184204	Point	Automated	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt736_ts_002
101virus-like capsid Annotation ID: AN-184203	Point	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt736_ts_002
100virus-like capsid Annotation ID: AN-184202	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt736_ts_002
102virus-like capsid Annotation ID: AN-184200	Point	Automated	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt735_ts_002
101virus-like capsid Annotation ID: AN-184199	Point	Hybrid	Dataset: PP7 virus-like particles in E. coli imaged with the crossed laser phase plate (xLPP) at 0.5-1.5 µm underfocus Run: pt735_ts_002