EMPIAR-12512 - Cryo-electron tomography of neuronal synapses, Munc13-SNAP25 project [multiple data sets in MRCS and MRC formats]

EMPIAR-12512

Cryo-electron tomography of neuronal synapses, Munc13-SNAP25 project [multiple data sets in MRCS and MRC formats]

Publication:

Munc13- and SNAP25-dependent molecular bridges play a key role in synaptic vesicle priming

Papantoniou C, Laugks U, Betzin J, Capitanio C, Ferrero JJ, Sánchez-Prieto J, Schoch S, Brose N, Baumeister W, Cooper BH, Imig C, Lučić V

Science advances 9 (2023)

PMID: 37343100

DOI: 10.1126/sciadv.adf6222

Related EMDB entry:

EMD-52342 EMD-52343

Deposited:

2024-12-15

Released:

2026-01-05

Last modified:

2026-01-05

Imageset size:

263.41 GB

Imageset DOI:

10.6019/EMPIAR-12512

Experimental metadata:

Download xml json

Contains:

tilt series
reconstructed volumes

Image Sets

1. Aligned series set 1, bin-1

Category:

tilt series

Image format:

MRCS

No. of images or tilt series:

Image size:

(3712, 3712)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(4.39, 4.39)

Details:

The first set of aligned series, containing 40 out of 80 series. Frames were aligned using MotionCor2 and aligned based on fiducial markers using IMOD.

Files:

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2. Aligned series set 2, bin-2

Category:

tilt series

Image format:

MRCS

No. of images or tilt series:

Image size:

(1856, 1856)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(8.78, 8.78)

Details:

The second set of aligned series, containing the other 40 out of 80 series. Frames were aligned using MotionCor2 and aligned based on fiducial markers using IMOD.

Files:

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)

3. Tomograms bin-4

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(928, 928)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(17.56, 17.56)

Details:

Tomograms reconstructed from the two sets of aligned series. There are 82 tomograms because there are 80 tilt series and two tilt series contain two synapses each (other series contain one synapse each). Tomograms were reconstructed by WBP (ramp filter) in IMOD. No further processing was performed (such as filtering, or denoising).

Files:

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)

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Citations

GTpick: A deep neural network for Cryo-EM particle detection.

Ni S, Yang C, Liu Y, Zhang Y, Shi Y, Qian A, Kong R, Chang S. (2025)

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Kim K, Li H, Clarke OB. (2025)

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.

Krentzel D, Elphick M, Domart MC, Peddie CJ, Laine RF, Shand C, Henriques R, Collinson LM, Jones ML. (2025)

CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.

Arora S, Pan SH, Kumar S, Singh SK, Chauhan U, Alhalabi W, Arya V, Alsulami BS, Hsu CH, Chui KT, Gupta BB. (2025)

PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.

Costa-Gomes B, Greer J, Juraschko N, Parkhurst J, Mirecka J, Famili M, Rangel-Smith C, Strickson O, Lowe A, Basham M, Burnley T. (2025)

DiameTR: A cryo-EM tool for diameter sorting of tubular samples.

Peng R, Elkhaligy H, Grant T, Stagg SM. (2025)

Self-supervised learning for generalizable particle picking in cryo-EM micrographs.

Zamanos A, Koromilas P, Bouritsas G, Kastritis PL, Panagakis Y. (2025)

Localization of macromolecules in crowded cellular cryo-electron tomograms from extremely sparse labels.

Uddin MR, Ahmed AY, Tabib HMS, Tahmid MT, Alam MZU, Freyberg Z, Xu M. (2025)

Structural insight into bicarbonate-mediated carboxylation by human vitamin K-dependent carboxylase.

Wu K, Wang Z, Yao D, Li S, Wang X, Zhang Y, Cao M, Shen Y, Xing S, Wu J, Lei M, Lan P. (2025)

Conserved hydrophilic checkpoints tune FocA-mediated formate:H<sup>+</sup> symport.

Tüting C, Janson K, Kammel M, Ihling C, Lorenz J, Kyrilis FL, Hamdi F, Erdmann C, Sinz A, Sawers RG, Kastritis PL. (2025)

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