EMPIAR-12177 - Cryo-ET dataset (3) of dormant microporidian spores from Encephalitozoon intestinalis [multiple data sets in TIFF and MRC formats]

EMPIAR-12177

Cryo-ET dataset (3) of dormant microporidian spores from Encephalitozoon intestinalis [multiple data sets in TIFF and MRC formats]

Publication:

Cryo-ET reveals the in situ architecture of the polar tube invasion apparatus from microsporidian parasites

Usmani M, Coudray N, Riggi M, Raghu R, Ramchandani H, Bobe D, Kopylov M, Zhong ED, Iwasa JH, Ekiert DC, Bhabha G

(---)

DOI: 10.1101/2024.07.13.603322v1

Related EMDB entry:

EMD-45671 EMD-45672

Deposited:

2024-06-03

Released:

2025-05-22

Last modified:

2025-05-22

Imageset size:

1.14 TB

Imageset DOI:

10.6019/EMPIAR-12177

Experimental metadata:

Download xml json

Contains:

tilt series
reconstructed volumes

Image Sets

1. Raw frames from dataset 3 of microsporidian Encephalitozoon intestinalis

Category:

tilt series

Image format:

TIFF

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(3.431, 3.431)

Details:

Each tilt series is contained within its unique directory with an identifiable name. The folder called 'raw_frames' contains the raw frames and corresponding mdoc field from each tilt series. The aligned tilt series file can be found in 'aligned_tilt_series'.

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. Unaligned tilt stacks from dataset 3 of microsporidian Encephalitozoon intestinalis

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(3.431, 3.431)

Details:

Each tilt series is contained within its unique directory with an identifiable name. The folder called 'tilt_series' contains the unaligned tilt stacks with corresponding tilt files. The aligned tilt series can be found in 'aligned_tilt_series'.

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)

3. Reconstructed tomograms from dataset 3 of microsporidian Encephalitozoon intestinalis

Category:

reconstructed volumes

Image format:

MRC

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(None, None)

Details:

Each tomogram reconstruction is contained within its unique directory with an identifiable name. The folder called 'tomo_rec_4bin_SART' contains the 4 times binned volume reconstructed using aretomo as examples.

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

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

See all citations

Protein Data Bank Japan News

[2025-05-28]

250 new PDB entries have been released on 2025-05-28.

[2025-04-18]

[wwPDB] Download Snapshots of the PDB Core Archive via HTTPS, SYNC, RSYNC, or FTP

[2025-03-25]

Announcement of the PDBj Newsletter Vol.25 release

[2025-03-11]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

[2025-03-10]

[wwPDB] New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models