EMPIAR-11618 - Single-particle cryo-EM dataset of an asymmetric nucleosome (10-N-0) [multiple data sets in TIFF and MRCS formats]

EMPIAR-11618

Single-particle cryo-EM dataset of an asymmetric nucleosome (10-N-0) [multiple data sets in TIFF and MRCS formats]

Publication:

Structure and dynamics of the chromatin remodeler ALC1 bound to a PARylated nucleosome

Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S

eLife 10 (2021)

PMID: 34486521

DOI: 10.7554/elife.71420

Related EMDB entry:

EMD-17944

Deposited:

2023-07-05

Released:

2023-08-25

Last modified:

2023-08-25

Imageset size:

1.15 TB

Imageset DOI:

10.6019/EMPIAR-11618

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned movies

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1537

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(0.952, 0.952)

Details:

The pixel size of 0.9783 A/pix in the tiff header is wrong, the correct one is 0.952 as indicated in the deposition metadata. This discrepancy comes from the fact that this dataset was collected during commissioning of the microscope, before the pixel size at this magnification was calibrated.

The coordinates deposited here are the particles that gave the reconstruction deposited as EMD-17944.

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.

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. Extracted particles

Category:

picked particles - single frame - processed

Image format:

MRCS

No. of images or tilt series:

68401

Image size:

(256, 256)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.952, 0.952)

Details:

Particle stack extracted from motion-corrected micrographs. Running ab initio reconstruction and 3D refinement on them should reproduce the reconstruction deposited as EMD-17944.

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)

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

[2025-02-05]

286 new PDB entries have been released on 2025-02-05.

[2025-01-30]

[wwPDB] Take the PDBx/mmCIF User Guide Survey and Win!

[2025-01-17]

[wwPDB] PDB-Dev now PDB-IHM

[2025-01-09]

[wwPDB] Time-stamped Copies of PDB and EMDB Archives

[2024-11-28]

[wwPDB] Access SDF/MOL formatted CCD files from the PDB archive