EMPIAR-11765 - Single-particle cryo electron microscopy of Integrin a4b7 bound to MadCAM-1 [multiple data sets in TIFF, MRC and MRCS formats]

EMPIAR-11765

Single-particle cryo electron microscopy of Integrin a4b7 bound to MadCAM-1 [multiple data sets in TIFF, MRC and MRCS formats]

Publication:

Molecular exaptation by the integrin αI domain

Hollis JA, Malik HS, Campbell MG, Chan MC

(---)

DOI: 10.1126/sciadv.adx9567

Related EMDB entry:

EMD-71399

Deposited:

2023-11-03

Released:

2025-11-21

Last modified:

2025-11-21

Imageset size:

3.45 TB

Imageset DOI:

10.6019/EMPIAR-11765

Experimental metadata:

Download xml json

Contains:

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

Image Sets

1. Unaligned multi-frame movies of integrin a4b7 bound to MadCAM-1

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

3223

Image size:

(5760, 4092)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(0.561, 0.561)

Details:

α4β7 integrin bound to MadCAM-1: 3223 unaligned uncorrected movies collected in two different datasets (803 + 2420) were recorded automatically using SerialEM on a K3 camera in super-resolution mode on a Glacios microscope operated at 200 kV (Cs=2.7). The movies contain 100 frames and the super resolution pixel size is 0.561 Å/px. The total dose per movie is ~50 e/Å^2. The gain reference is also included for each dataset in .dm4 format; 20220516_K3GainRefx1m3.dm4 is used to reference movies 20220517**.tif and 20220522_K3GainRefx1m3.dm4 is used to reference movies 20220525**.tif.

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2. Dose-weighted aligned micrographs of integrin a4b7 bound to MadCAM-1

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

3223

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.122, 1.122)

Details:

α4β7 integrin bound to MadCAM-1: 3223 unaligned uncorrected movies collected over 2 datasets (803 + 2420) were recorded automatically using SerialEM on a K3 camera in super-resolution mode on a Glacios microscope operated at 200 kV (Cs=2.7). The total dose per micrograph is ~50 e/Å^2. Images were dose-weighted and motion-corrected in MotionCor2 via the RELION GUI. Images were binned by 2 using Fourier cropping and the binned pixel size is 1.122.

Files:

This entry cannot be downloaded from PDBj.

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3. Dose-weighted aligned particle stacks of clasped apo-integrin a4b7 in the compact state

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

188443

Image size:

(364, 364)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.122, 1.122)

Details:

Stacks of 188443 particles selected after sequential 2D and 3D classification contributing to final reconstruction of α4β7 integrin bound to MadCAM-1. Unaligned uncorrected movies were recorded automatically using SerialEM on a K3 camera in super-resolution mode on a Glacios microscope operated at 200 kV (Cs=2.7). The total dose per micrograph is ~50 e/Å^2. Images were dose-weighted and motion-corrected in MotionCor2 via the RELION GUI. Images were binned by 2 using Fourier cropping and the binned pixel size is 1.122.

Files:

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Citations

GTpick: A deep neural network for Cryo-EM particle detection.

Ni S, Yang C, Liu Y, Zhang Y, Shi Y, Qian A, Kong R, Chang S. (2025)

High-resolution ab initio reconstruction enables cryo-EM structure determination of small particles

Kim K, Li H, Clarke OB. (2025)

CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy.

Krentzel D, Elphick M, Domart MC, Peddie CJ, Laine RF, Shand C, Henriques R, Collinson LM, Jones ML. (2025)

PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modeling and machine learning.

Costa-Gomes B, Greer J, Juraschko N, Parkhurst J, Mirecka J, Famili M, Rangel-Smith C, Strickson O, Lowe A, Basham M, Burnley T. (2025)

CryoEMNet driven symmetry-aware molecular reconstruction through deep learning enhanced electron microscopy.

Arora S, Pan SH, Kumar S, Singh SK, Chauhan U, Alhalabi W, Arya V, Alsulami BS, Hsu CH, Chui KT, Gupta BB. (2025)

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Tüting C, Janson K, Kammel M, Ihling C, Lorenz J, Kyrilis FL, Hamdi F, Erdmann C, Sinz A, Sawers RG, Kastritis PL. (2025)

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