Deposition

In situ cryo-electron tomography of the nuclear pore complex in NIH/3T3 fibroblasts

Deposition ID:CZCDP-10365

Release Date: 2026-08-31

Last Modified: 2026-08-31

key visualization for In situ cryo-electron tomography of the nuclear pore complex in NIH/3T3 fibroblasts

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

Deposition Overview

Cryo-electron tomograms of cryo-FIB-milled lamellae through intact, plunge-frozen NIH/3T3 mouse fibroblasts, collected across three acquisition sessions and capturing the nuclear envelope in a near-native state. The nuclear pore complexes in these tomograms supported a subtomogram-averaged map of the mammalian nuclear pore and the molecular architecture of its nuclear basket.

Authors

Deposition Data

Annotations:240

Tomograms:480

Publications

DOI:10.1016/j.cell.2024.07.020
DOI:10.1101/2024.03.27.587068

Related Databases

EMDB ID:EMD-44379

Methods Summary

Annotations	Method Type	Method Details	Method Links
120	Automated	A mesh marking the valid sample region of each lamella. A sample/vacuum boundary was predicted with octopi on a downsampled reconstruction, and a spline slab was fitted to that boundary and intersected with the tomogram's valid-area box to give the enclosing surface.	Source Code:copick +2 more
120	Automated	Prediction using membrain-seg without rescaling and weights MemBrain_seg_v10_alpha.ckpt	Source Code:copick +4 more

Deposited Data

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Data Contents

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240 of 240 Annotations

Annotation Name	Object Shape Type	Method Type	Deposited In
101sample Annotation ID: AN-182012	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_013
100membrane Annotation ID: AN-182011	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_013
101sample Annotation ID: AN-182010	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_012
100membrane Annotation ID: AN-182009	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_012
101sample Annotation ID: AN-182008	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_011
100membrane Annotation ID: AN-182007	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_011
101sample Annotation ID: AN-182006	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_010
100membrane Annotation ID: AN-182005	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_010
101sample Annotation ID: AN-182004	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_009
100membrane Annotation ID: AN-182003	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_009
101sample Annotation ID: AN-182002	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_008
100membrane Annotation ID: AN-182001	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_008
101sample Annotation ID: AN-182000	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_007
100membrane Annotation ID: AN-181999	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_007
101sample Annotation ID: AN-181998	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_006
100membrane Annotation ID: AN-181997	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_006
101sample Annotation ID: AN-181996	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_005
100membrane Annotation ID: AN-181995	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_005
101sample Annotation ID: AN-181994	Mesh	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_004
100membrane Annotation ID: AN-181993	SegmentationMask	Automated	Dataset: Cryo-FIB-milled NIH/3T3 mouse fibroblasts (dataset 5)Run: L9_ts_004