EMPIAR-13331 - Cryo electron tomography of BG505 HIV-1 Env in a virus-like particle [multiple data sets in EER format]

EMPIAR-13331

Cryo electron tomography of BG505 HIV-1 Env in a virus-like particle [multiple data sets in EER format]

Publication:

N-Glycans Modulate HIV-1 Env Conformational Plasticity

Shehata M, Casalino L, Duquette M, Chen S, Flaherty A, Villa E, Amaro RE

bioRxiv (2025)

DOI: 10.1101/2025.03.26.645577

Related EMDB entry:

EMD-75641

Deposited:

2025-11-06

Released:

2026-04-09

Last modified:

2026-04-09

Imageset size:

962.95 GB

Imageset DOI:

10.6019/EMPIAR-13331

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Raw cryoET data from collection on 7/18/2025

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

4012

Image size:

(4096, 4096)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.561, 1.561)

Details:

There are 224 EER frames per image, and each tilt series is comprised of up to 37 tilts. Some of them have fewer tilts because the stage has a maximum tilt angle and some of the targets had a larger estimated pre-tilt while setting up paceTOMO. Associated metadata from SerialEM is in the mdocs folder.

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2. Raw cryoET data from collection on 7/19/2025

Category:

micrographs - multiframe

Image format:

EER

No. of images or tilt series:

5884

Image size:

(4096, 4096)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.561, 1.561)

Details:

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)

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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)