Deposition

In situ virus-like particles in E. coli for microscopy and pipeline benchmarking

Deposition ID:CZCDP-10336

Release Date: 2025-11-07

Last Modified: 2026-05-13

key visualization for In situ virus-like particles in E. coli for microscopy and pipeline benchmarking

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

Deposition Overview

Datasets described in manuscript "Characterization Standard for In-situ Cryo-electron Tomography". The PP7 bacteriophage virus-like particles form highly symmetric capsids that are suitable for high-resolution structure determination. These datasets were collected on E. coli overexpressing the VLPs, therefore, providing a thick crowded in situ sample that is suitable for benchmarking cryoET applications including both data collection and data processing.

Authors

Deposition Data

Annotations:2,108

Tomograms:1,694

Publications

DOI:10.64898/2026.05.20.726049

Related Databases

EMDB ID:EMD-77085

Methods Summary

Annotations	Method Type	Method Details	Method Links
290	Hybrid	octopi prediction + 3D refinement (RELION)	Source Code:Octopi +6 more
176	Hybrid	octopi prediction + 2D/3D classification and refinement (RELION) + max likelihood filtering	Source Code:Octopi +2 more
233	Hybrid	pytom-match-pick template matching + octopi prediction + 2D classification	Source Code:pytom-match-pick +4 more
306	Hybrid	octopi prediction + 3D refinement (RELION) + max likelihood filtering	Source Code:Octopi +2 more
124	Hybrid	octopi prediction + 2D classification + 3D refinement (RELION)	Source Code:Octopi +6 more
260	Hybrid	octopi prediction + 2D classification and refinement (RELION) + max likelihood filtering	Source Code:Octopi +2 more
402	Automated	octopi prediction	Source Code:Octopi +3 more
314	Automated	Prediction using membrain-seg without rescaling and weights MemBrain_seg_v10_alpha.ckpt	Source Code:membrain-seg +1 more
3	Automated	manual picking in ChimeraX-copick	Not Submitted

Deposited Data

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Data Contents

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2,108 of 2,108 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
100Capsid protein Annotation ID: AN-135706 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_9
100Capsid protein Annotation ID: AN-135705 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_8
100Capsid protein Annotation ID: AN-135704 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_7
100Capsid protein Annotation ID: AN-135703 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_6
100Capsid protein Annotation ID: AN-135702 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_4
100Capsid protein Annotation ID: AN-135701 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_3
100Capsid protein Annotation ID: AN-135700 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_2
100Capsid protein Annotation ID: AN-135699 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_13
100Capsid protein Annotation ID: AN-135698 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_12
100Capsid protein Annotation ID: AN-135697 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_11
100Capsid protein Annotation ID: AN-135696 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9_10
100Capsid protein Annotation ID: AN-135695 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_9
100Capsid protein Annotation ID: AN-135694 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_9
100Capsid protein Annotation ID: AN-135693 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_8
100Capsid protein Annotation ID: AN-135692 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_7
100Capsid protein Annotation ID: AN-135691 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_6
100Capsid protein Annotation ID: AN-135690 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_5
100Capsid protein Annotation ID: AN-135689 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_4
100Capsid protein Annotation ID: AN-135688 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_3
100Capsid protein Annotation ID: AN-135687 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E. coli at 3.9 Å (lamellae)Run: 26feb20d_Position_6_2