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: 2025-11-07

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

The bacteriphage virus-like particles form highly symmetric capsids that are suitable for high-resolution structure determination (cite). 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:1,059

Tomograms:628

Publications

DOI:10.1021/acsnano.8b09683
DOI:10.1021/acsnano.3c06178

Related Databases

EMDB ID:EMD-44783

Methods Summary

Annotations	Method Type	Method Details	Method Links
306	Hybrid	octopi prediction + 3D refinement (RELION) + max likelihood filtering	Source Code:Octopi +2 more
176	Hybrid	octopi prediction + 2D/3D classification and refinement (RELION) + max likelihood filtering	Source Code:Octopi +2 more
260	Hybrid	octopi prediction + 2D classification and refinement (RELION) + max likelihood filtering	Source Code:Octopi +2 more
314	Automated	Prediction using membrain-seg without rescaling and weights MemBrain_seg_v10_alpha.ckpt	Source Code:membrain-seg +1 more
3	Manual	manual picking in ChimeraX-copick	Source Code:Copick +2 more

Deposited Data

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Data Contents

Tilt SeriesAvailable

FramesAvailable

CTFAvailable

AlignmentAvailable

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1,059 of 1,059 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
103Capsid protein Annotation ID: AN-103529 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_9_3
102Capsid protein Annotation ID: AN-103528 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_9_3
101Capsid protein Annotation ID: AN-103527 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_9_3
103Capsid protein Annotation ID: AN-103525 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_9_2
102Capsid protein Annotation ID: AN-103524 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_9_2
101Capsid protein Annotation ID: AN-103523 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_9_2
103Capsid protein Annotation ID: AN-103521 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_99_2
102Capsid protein Annotation ID: AN-103520 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_99_2
101Capsid protein Annotation ID: AN-103519 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_99_2
103Capsid protein Annotation ID: AN-103517 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_99
102Capsid protein Annotation ID: AN-103516 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_99
101Capsid protein Annotation ID: AN-103515 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_99
103Capsid protein Annotation ID: AN-103513 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_98
102Capsid protein Annotation ID: AN-103512 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_98
101Capsid protein Annotation ID: AN-103511 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_98
103Capsid protein Annotation ID: AN-103509 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_97_2
102Capsid protein Annotation ID: AN-103508 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_97_2
101Capsid protein Annotation ID: AN-103507 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_97_2
103Capsid protein Annotation ID: AN-103505 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_97
102Capsid protein Annotation ID: AN-103504 Ground Truth	OrientedPoint	Hybrid	Dataset: PP7 virus-like particles in E.Coli at 3.3 Å Run: 25aug25a_Position_97