EMPIAR-10264 - LAT1-CD98hc bound to MEM-108 Fab [multiple data sets in TIFF and MRCS formats]

EMPIAR-10264

LAT1-CD98hc bound to MEM-108 Fab [multiple data sets in TIFF and MRCS formats]

Publication:

Cryo-EM structure of the human L-type amino acid transporter 1 in complex with glycoprotein CD98hc

Lee Y, Wiriyasermkul P, Jin C, Quan L, Ohgaki R, Okuda S, Kusakizako T, Nishizawa T, Oda K, Ishitani R, Yokoyama T, Nakane T, Shirouzu M, Endou H, Nagamori S, Kanai Y, Nureki O

Nature structural & molecular biology (2019)

PMID: 31160781

DOI: 10.1038/s41594-019-0237-7

Related EMDB entry:

EMD-9849

Deposited:

2019-03-24

Released:

2019-07-25

Last modified:

2019-08-16

Imageset size:

4.08 TB

Imageset DOI:

10.6019/EMPIAR-10264

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame micrographs, Dataset1

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1582

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(0.8346, 0.8346)

Details:

Unaligned, gain corrected movies from Falcon 3 in the counting mode. The MRC files from EPU were converted to the TIFF format by mrc2tif in IMOD. During this process, the pixel size in the image header became 1.0. The calibrated pixel size is 0.8346. The total exposure is 46.0 electrons per squared Angstom in a 46.5 second exposure. The data contain a few dozen micrographs that were excluded during the processing due to poor maximal CTF resolution.

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2. Unaligned multi-frame micrographs, Dataset2

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1900

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(0.8346, 0.8346)

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.

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3. Micelle subtracted particles used for final reconstruction

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

361967

Image size:

(288, 288)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.333, 1.333)

Details:

Micelle subtracted particles used for final reconstruction. The MRCS file contains 361,967 particles but some were rejected during classification. The final set of particles and the orientations are stored in the associated STAR file. The image header contains a wrong pixel size information (1.375 A) because of the assumed nominal pixel size (0.861 A). The actual calibrated pixel size is 1.333 A (0.8346 A x 460 pix / 288 pix due to down-sampling), which is used for the final reconstruction in the associated publication.

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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Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

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