EMPIAR-10433 - Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis [multiple data sets in TIFF and MRC formats]

EMPIAR-10433

Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis [multiple data sets in TIFF and MRC formats]

Publication:

Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis

Herrera NG, Morano NC, Celikgil A, Georgiev GI, Malonis R, Lee JH, Tong K, Vergnolle O, Massimi A, Yen LY, Noble AJ, Kopylov M, Bonanno JB, Garrett-Thomson SC, Hayes DB, Bortz R, Wirchnianski A, Florez C, Laudermilch E, Haslwanter D, Fels J, Dieterle M, Jangra R, Barnhill J, Mengotto A, Kimmel D, Daily J, Pirofski L, Chandran K, Brenowitz M, Garforth S, Eng E, Lai JR, Almo SC

ACS omega (2020)

DOI: 10.1021/acsomega.0c03512

Related EMDB entry:

EMD-22078

Deposited:

2020-05-29

Released:

2020-06-16

Last modified:

2021-01-22

Imageset size:

484.30 GB

Imageset DOI:

10.6019/EMPIAR-10433

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame

Image Sets

1. Unaligned multi frame micrographs of SARS CoV-2 SPIKE protein produced in CHO cells

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1280

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(None, None)

Details:

Topaz picking model exported from CryoSPARC. To use the model, you can:
1) Import it back into CryoSPARC by following these instructions: https://discuss.cryosparc.com/t/import-the-topaz-covid-19-spike-picking-model-to-use-in-your-projects/4708
2) Use the Topaz .sav file (located in P257_J75_topaz_model/J75/models/model_epoch11.sav) to pick with the Topaz standalone GUI or any other software that integrates Topaz (e.g. Relion or Scipion).

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.

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rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

2. Processed data - aligned frame sum with dose-weighting

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

1280

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.058, 1.058)

Details:

The high mag images (-a-DW.mrc) are 66.49 e-/A2 dose at 1.058Å/px with a dimension of 5760x4092px

Topaz picking model exported from CryoSPARC. To use the model, you can:
1) Import it back into CryoSPARC by following these instructions: https://discuss.cryosparc.com/t/import-the-topaz-covid-19-spike-picking-model-to-use-in-your-projects/4708
2) Use the Topaz .sav file (located in P257_J75_topaz_model/J75/models/model_epoch11.sav) to pick with the Topaz standalone GUI or any other software that integrates Topaz (e.g. Relion or Scipion).

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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Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

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)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

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