EMPIAR-11335 - Cryo-EM SPA datasets for Antibodies 12-16 & 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein (K3 movies/.tif files) [multiple data sets in TIFF format]

EMPIAR-11335

Cryo-EM SPA datasets for Antibodies 12-16 & 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein (K3 movies/.tif files) [multiple data sets in TIFF format]

Publication:

Antibodies targeting a quaternary site on SARS-CoV-2 spike glycoprotein prevent viral receptor engagement by conformational locking

Liu L, Casner RG, Guo Y, Wang Q, Iketani S, Chan JF, Yu J, Dadonaite B, Nair MS, Mohri H, Reddem ER, Yuan S, Poon VK, Chan CC, Yuen KY, Sheng Z, Huang Y, Bloom JD, Shapiro L, Ho DD

Immunity (2023)

PMID: 37776849

DOI: 10.1016/j.immuni.2023.09.003

Related EMDB entry:

EMD-26584 EMD-26583

Deposited:

2022-12-02

Released:

2023-10-09

Last modified:

2023-10-09

Imageset size:

2.59 TB

Imageset DOI:

10.6019/EMPIAR-11335

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. K3 Movies (.tif) for 12-16 Antibody + Spike

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

4088

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.83, 0.83)

Details:

Collected on a Krios using a K3 BioQuantum.
The gain reference is in data/12-16/day1/references/*norm_0.mrc.

Files:

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. K3 Movies (.tif) for 12-19 Antibody + Spike

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

7099

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.83, 0.83)

Details:

Collected on a Krios using a K3 BioQuantum.
day 1 has thinner ice and less particles.
day 2 has thicker ice and more particles.
The gain reference is in data/12-19/day2/references/*norm_0.mrc.

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)

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

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)