EMPIAR-10229 - Cryo-EM Reconstruction of apo EsCas13d [multiple data sets in MRCS format]

This entry has been removed from PDBj storage. Please download it from EMPIAR-EBI.

EMPIAR-10229

Cryo-EM Reconstruction of apo EsCas13d [multiple data sets in MRCS format]

Publication:

Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d

Zhang C, Konermann S, Brideau N, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin P, Hsu PD, Lyumkis D

Cell 175 (2018) 212-223

PMID: 30241607

DOI: 10.1016/j.cell.2018.09.001

Related EMDB entry:

EMD-9015

Deposited:

2018-11-13

Released:

2018-11-23

Last modified:

2018-11-23

Imageset size:

66.89 GB

Imageset DOI:

10.6019/EMPIAR-10229

Experimental metadata:

Download xml json

Contains:

picked particles - single frame - unprocessed
picked particles - single frame - processed

Image Sets

1. stack of ~150k particles used for ab initio orientation assignment and reconstruction

Category:

picked particles - single frame - unprocessed

Image format:

MRCS

No. of images or tilt series:

154889

Image size:

(320, 320)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.73, 0.73)

Details:

This directory contains a stack and associated .star file of 154,889 particles. This stack was used as input to common-lines-based ab initio 3D orientation assignment and reconstruction in cryoSparc. The procedure resulted in the automated selection of 15,846 particles, from which a reconstruction was performed. This reconstruction is reported in the associated publication and in EMD-9015.

Files:

This entry cannot be downloaded from PDBj.

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. stack of ~16k best particles from above

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

15846

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.73, 0.73)

Details:

This directory contains a stack and associated .star file of the 15,846 best particles selected from the full stack. This stack represents the clean particles from above and reproduces the deposited map when subjected to an ab initio orientation assignment and reconstruction procedure.

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)

Browse All Files

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

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)

See all citations

Protein Data Bank Japan News

[2024-11-20]

224 new PDB entries have been released on 2024-11-20.

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024