EMPIAR-11411 - Molecular mechanism of Trypanosoma brucei Aquaporin 2 with melarsoprol [multiple data sets in MRC and MRCS formats]

EMPIAR-11411

Molecular mechanism of Trypanosoma brucei Aquaporin 2 with melarsoprol [multiple data sets in MRC and MRCS formats]

Publication:

Insights from aquaporin structures into drug-resistant sleeping sickness

Mutusevicius M, Corey RA, Gragera M, Yamashita K, Sprenger T, Ungogo MA, Blaza JM, Castro-Hartmann P, Chirgadze DY, Vedithi SC, Afanasyev P, Melero R, Warshamanage R, Gusach A, Carazo JM, Carrington M, Blundell TM, Murshudov G, Stansfeld P, Sansom M, De Koning HP, Tate CG, Weyand SN

eLife RP107460 (2025)

DOI: 10.7554/eLife.107460.1

Related EMDB entry:

EMD-16862

Deposited:

2023-01-23

Released:

2025-10-23

Last modified:

2025-10-23

Imageset size:

1.20 TB

Imageset DOI:

10.6019/EMPIAR-11411

Experimental metadata:

Download xml json

Compressed by PDBj:

Image formats and pixel types shown below are those of the original, non-compressed files.

Movies (Export/Images-Disc1/GridSquare_*/Data/FoilHole_*.mrc) in this entry were compressed to TIFF
by EMPIAR Japan to save space and bandwidth.
The compression is lossless in that all pixel intensities remain exactly the same after decompression.
However, some metadata in the MRC header were lost.
The original files before compression are available from EMPIAR EBI.

Compression was carried out by separating (“un-normalizing”) the gain.
The details of the method are described in
https://relion.readthedocs.io/en/release-3.1/Reference/MovieCompression.html#gain-normalised-movies.

Please apply the gain reference (Export/Images-Disc1/gain-reference.mrc) during processing.

PDBj discovered that this entry contained one RSYNC temporary file
(Export/Images-Disc1/GridSquare_7402420/Data/.FoilHole_7409440_Data_7416445_7416446_20190210_1558-136921.mrc.0u7lsa)
and removed it.

Original size:   9,089,188,178 kilobytes
Compressed size: 1,014,695,568 kilobytes

Contains:

micrographs - single frame
picked particles - single frame - processed
micrographs - multiframe

Image Sets

1. Aligned dose-weighted micrographs of Aqp2 + melarsoprol from Trypanosoma brucei (MotionCorr2 output)

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

4087

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.07, 1.07)

Details:

Aligned (all frames) and dose-weighted micrographs from MotionCorr2

Files:

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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. Particle set of the final 3D reconstruction of Aqp2 + melarsoprol from Trypanosoma brucei

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

126551

Image size:

(320, 320)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.07, 1.07)

Details:

Particles that yielded the final 3D reconstruction of Aqp2 + melarsoprol.

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. Raw movies of Aqp2 + melarsoprol from Trypanosoma brucei

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

4087

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.07, 1.07)

Details:

---

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

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2026)

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)