EMPIAR-13332 - Cryo-EM structures of alpha5beta1 integrin in complex with NeoNectin candidate 2, open and closed conformation [multiple data sets in TIFF and MRC formats]

EMPIAR-13332

Cryo-EM structures of alpha5beta1 integrin in complex with NeoNectin candidate 2, open and closed conformation [multiple data sets in TIFF and MRC formats]

Publication:

De Novo Design of Integrin α5β1 Modulating Proteins to Enhance Biomaterial Properties

Wang X, Guillem-Marti J, Kumar S, Lee DS, Cabrerizo-Aguado D, Werther R, Alamo KAE, Zhao YT, Nguyen A, Kopyeva I, Huang B, Li J, Hao Y, Li X, Brizuela-Velasco A, Murray A, Gerben S, Roy A, DeForest CA, Springer T, Ruohola-Baker H, Cooper JA, Campbell MG, Manero JM, Ginebra MP, Baker D

Advanced materials (Deerfield Beach, Fla.) 37 (2025) e2500872-N/A

PMID: 40489013

DOI: 10.1002/adma.202500872

Related EMDB entry:

EMD-46902 EMD-47968

Deposited:

2025-04-29

Released:

2026-03-23

Last modified:

2026-03-23

Imageset size:

1.12 TB

Imageset DOI:

10.6019/EMPIAR-13332

Experimental metadata:

Download xml json

Contains:

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

Image Sets

1. Unaligned multi-frame images of integrin alpha5 beta1 and minibinder

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1230

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.561, 0.561)

Details:

One hundred frame movies were recorded in super-resolution mode with a super-resolution pixel size of 0.561 Å/px, a nominal magnification of 36kx, a nominal defocus range of 1.2 to 2.0 µm under focus, and an approximate dose of 50 electrons per square Å

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2. Aligned particle stacks of alpha5 beta1 integrin bound to minibinder for open conformation

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

63256

Image size:

(352, 352)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.122, 1.122)

Details:

Polished particles in .mrc format for open conformation and accompanying metadata in .star file

Files:

This entry cannot be downloaded from PDBj.

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3. Movie gain refs

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

Image size:

(11520, 8184)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.556, 0.556)

Details:

Gain reference for movie collection in mrc format

Files:

This entry cannot be downloaded from PDBj.

Archives and downloads the selected files into an uncompressed zip file.

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4. Aligned particle stacks of alpha5 beta1 integrin bound to minibinder for closed conformation

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

153759

Image size:

(352, 352)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.122, 1.122)

Details:

Polished particles in .mrc format for closed conformation and metadata in accompanying .star file

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)