EMPIAR-11745 - In vitro TDP-43 amyloid fibrils [1641 multi-frame micrographs composed of 40 frames each in TIFF format]

EMPIAR-11745

In vitro TDP-43 amyloid fibrils [1641 multi-frame micrographs composed of 40 frames each in TIFF format]

Publication:

Cryo-EM observation of the amyloid key structure of polymorphic TDP-43 amyloid fibrils

Sharma K, Stockert F, Shenoy J, Berbon M, Abdul-Shukkoor MB, Habenstein B, Loquet A, Schmidt M, Fändrich M

Nature communications 15 (2024)

PMID: 38212334

DOI: 10.1038/s41467-023-44489-0

Related EMDB entry:

EMD-18717 EMD-18715 EMD-18716

Deposited:

2023-08-03

Released:

2024-06-04

Last modified:

2024-06-04

Imageset size:

280.11 GB

Imageset DOI:

10.6019/EMPIAR-11745

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe

Image Sets

1. Unaligned multi-frame micrographs of TDP-43 amyloid fibrils

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

1641

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.04, 1.04)

Details:

The gain reference (/data/EM_data/CountRef_0001.dm4) is not applied to the raw micrographs. The NOTES.txt file contains EM information (copied below). The coordinates are divided into Morphology-1 (/data/Coordinatesfiles_Morphology1) and Morphology-2 (/data/Coordinatesfiles_Morphology2).

---------------------------------------------------------------------------------------------------------------------------------------------------------------------------
NOTES.txt

EMBL Heidelberg
Krios1 Quantum-K2
Cs 2.7
300kV EFTEM nanpprobe
x130k spot 8 beam size 650nm
c2=50 objective_aperture=100

GIF-K2 counting
10s exposure 40 frames
total dose at the sample 52.08e/A2
1 pixel = 1.04A
dose rate ~3-4 e/pix/s

defocus range -1.2 to -2.5

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)

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