EMPIAR-10633 - Cryo-electron tomography of the metazoan membrane-assembled retromer:SNX3 coat containing Wls cargo motif [multiple data sets in TIFF and MRC formats]

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

EMPIAR-10633

Cryo-electron tomography of the metazoan membrane-assembled retromer:SNX3 coat containing Wls cargo motif [multiple data sets in TIFF and MRC formats]

Publication:

Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly

Leneva N, Kovtun O, Morado DR, Briggs JAG, Owen DJ

Science advances 7 (2021)

PMID: 33762348

DOI: 10.1126/sciadv.abf8598

Related EMDB entry:

EMD-12222 EMD-12221 EMD-12220

Deposited:

2021-01-18

Released:

2021-04-14

Last modified:

2021-06-30

Imageset size:

764.90 GB

Imageset DOI:

10.6019/EMPIAR-10633

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
tilt series

Image Sets

1. Raw image frames for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

4844

Image size:

(11520, 8184)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.8505, 0.8505)

Details:

Unaligned superresolution frames not corrected for detector’s gain and defects. Ten frames were saved per each tilt image. The exposure dose per tilt image was 3.0 e/Å^2. Calibrated physical pixel size 1.701 Å. Movies are named as ts_[tilt stack ID]_[sequntial movie number]_[tilt angle].tif.
For gain reference, use data/correction/SuperRef_ts_01_14.dm4 for tilts ts_01 to 14, and data/correction/SuperRef_ts_16_126.dm4 for tilts ts_16 to 126. The defect file data/correction/Krios3_K3_SerialEM_defects.txt to be applied to all tilt series.

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. Corrected, aligned and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

113

Image size:

(5760, 4092)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.701, 1.701)

Details:

Corrected, aligned and order-sorted tilt series. The tilt-series were generated from raw frames (data/rawframes) by applying gain reference and defect corrections, motion correction and Fourier cropping to physical pixel size. No dose-filtering was applied. Defocus estimation was performed using IMOD ctfplotter on non-dose filtered aligned stacks (data/aligned_stacks). ETOMO generated tilt alignment using 10 nm gold fiducials tracking.

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)

3. Corrected, aligned, dose-filtered and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

113

Image size:

(5760, 4092)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(1.701, 1.701)

Details:

Dose-filtered aligned stacks.

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

[2024-11-06]

404 new PDB entries have been released on 2024-11-06.

[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