EMPIAR-13880 - Cryo-electron tomography data collected in the nucleolus of HeLa cells on cryo-FIB lamellae [multiple data sets in TIFF and MRC formats]

EMPIAR-13880

Cryo-electron tomography data collected in the nucleolus of HeLa cells on cryo-FIB lamellae [multiple data sets in TIFF and MRC formats]

Publication:

In-cell structures visualize human pre-ribosome assembly in the nucleolus

Zhao X, Hayashi Y, Fung HKH, Cuylen-Häring S, Mahamid J, Müller CW

Science (---)

Related EMDB entry:

EMD-59083 EMD-59069 EMD-59085 EMD-59077 EMD-59086 EMD-58993 EMD-59076 EMD-59082 EMD-59088 EMD-59070

Deposited:

2026-07-23

Released:

2026-10-22

Last modified:

2026-10-22

Imageset size:

1.82 TB

Imageset DOI:

10.6019/EMPIAR-13880

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
reconstructed volumes

Image Sets

1. Cryo-electron tomography data collected in the nucleolus of HeLa cells on cryo-FIB lamellae: frames

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

12825

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.425, 3.425)

Details:

frames: the raw frames before processing.
mdocs: original modc files for tilt series.
csv: bad tilts needs to be removed listed in csv files.
gain: gain reference.
defectmap: defect file for Gatan K3 camera.
warp_frameseries_xml: xml files with motion correction and CTF estimation information for the frames, can be used to generate tomostar files.
warp_tiltseries_xml: xml files with alignment and CTF estimation information for the tilts, can be used to reconstruct tomograms.
tlt_xf: rawtlt files and .xf files for tilt series alignment.
extracted_particels: original particle list extracted from template matching before 3D classification.
particles_M_Refine: particle list for the reconstruction of the final EM maps.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

2. Cryo-electron tomography data collected in the nucleolus of HeLa cells on cryo-FIB lamellae: reconstructions

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

398

Image size:

(1024, 1440)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(13.7, 13.7)

Details:

Path: /data/[date]/reconstruction. Recosntructed tomograms in WarpTools using the alignments in xml files listed in the same entry.

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

Browse All Files

Quick Links

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

Citations

Structural identification of the RY12 domain of RyR1 as an ADP sensor and the target of the malignant hyperthermia therapeutic dantrolene.

Kim K, Li H, Yuan Q, Melville Z, Zalk R, des Georges A, Frank J, Hendrickson WA, Marks AR, Clarke OB. (2026)

Post-acquisition super resolution for cryo-electron microscopy.

Burton Smith RN, Murata K. (2026)

Structural heterogeneity of CTE Type I tau filaments with an interface-shifted polymorph

Watanabe R, Lee EB. (2026)

CryoTriplane: Triplane-based Neural Radiance Field Representation for High-resolution Cryo-EM 3D Homogeneous Reconstruction.

Cheng Y, He B, Zeng Q, Zhang F, Han R. (2026)

Ligand-induced activation of RyR1 in native membranes.

Mikirtumov V, Golusik S, Huo R, Sprink T, Balyschew N, Yang W, Diebolder C, Yuan S, Kotecha A, Kudryashev M. (2026)

QwenCryoMarker: a universal post-processing framework for contamination-aware particle cleaning.

Sun Y, Zhao J, Xu N, Wang L, Ding W, Li M. (2026)

An unattended image-processing pipeline for on-the-fly quality assessment and 3D exploration in cryo-EM.

Marchán Torres D, Conesa P, Garcia A, Iceta M, Broche L, Gragera M, Linares R, Kwong HS, Chichón FJ, Svensson O, Arranz R, Effantin G, Kandiah E, Carazo JM, Sorzano COS. (2026)

CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM

Li F, Dong H, Tang S, Wang X, Zhang C, Ji C, Han R, Zhang F, Wan X. (2026)

Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging

So-Last MGF, Burt A, Hale T, Allegretti M. (2026)

AlignPCA-2D: PCA-reduced Euclidean vector alignment for 2D classification in cryo-EM.

Ramírez-Aportela E, Zarrabeitia OL, Fonseca YC, Ceska T, Subramaniam S, Carazo JM, Sorzano COS. (2026)

See all citations

Protein Data Bank Japan News

[2026-10-21]

244 new PDB entries have been released on 2026-10-21.

[2026-10-20]

[wwPDB] PDB's Emerald Anniversary