EMPIAR-10550 - Structure of the class D GPCR Ste2 dimer coupled to two G proteins [multiple data sets in MRC and TIFF formats]

EMPIAR-10550

Structure of the class D GPCR Ste2 dimer coupled to two G proteins [multiple data sets in MRC and TIFF formats]

Publication:

Structure of the class D GPCR Ste2 dimer coupled to two G proteins

Velazhahan V, Ma N, Pándy-Szekeres G, Kooistra AJ, Lee Y, Gloriam DE, Vaidehi N, Tate CG

Nature 589 (2020) 148-153

PMID: 33268889

DOI: 10.1038/s41586-020-2994-1

Related EMDB entry:

EMD-11720

Deposited:

2020-09-14

Released:

2020-12-04

Last modified:

2021-02-12

Imageset size:

1.28 TB

Imageset DOI:

10.6019/EMPIAR-10550

Experimental metadata:

Download xml json

Compressed by PDBj:

Image formats and pixel types shown below are those of the original, non-compressed files.

MRC movies (FoilHole*.mrc) in this entry were compressed by bzip2 (pbzip2)
by EMPIAR Japan to save space and bandwidth.

Some programs (e.g. RELION >= 4.0.1 and CryoSPARC) can process compressed movies without explicit
decompression. For other programs, movies have to be decompressed beforehand. In this case,
you might want to convert decompressed MRC movies into TIFF to save your local storage.

Original size:   6,466,617,150 kilobytes
Compressed size:   993,373,678 kilobytes

Contains:

micrographs - multiframe

Image Sets

1. LMB Krios1 Movies

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

996

Image size:

(3838, 3710)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(1.145, 1.145)

Details:

contains unaligned movies corresponding to the data collection "LMB Krios1". The real pixel size is 1.145 Å/pix, and the dose rate is 1.013 e/Å^2/frame. Please use data/LMB_Krios1_Movies/Micrographs/GainReference/FoilHole_16392868_Data_16385023_16385025_20191017_011206-gain-ref.MRC as gain reference without any rotation or flipping.

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. LMB Krios2 Movies

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

2027

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.1, 1.1)

Details:

contains unaligned movies corresponding to the data collection "LMB Krios2". The real pixel size is 1.1 Å/pix, and the dose rate is 1.015 e/Å^2/frame. Please use data/LMB_Krios2_Movies/Micrographs/h1_s1/CountRef_krios2_24102019_h1_s1_i0001_movie_Oct24_17.44.14.mrc as gain reference without any rotation or flipping. The defects file can be found at data/LMB_Krios2_Movies/Micrographs/h1_s1/defects_krios2_24102019_h1_s1_i0001_movie_Oct24_17.44.14.txt. The "_hn_sn_" ,where n=1-9, portion of the file name refers to the hole and shot position within 3x3 image shift acquisition matrix (two non-overlapping shots per hole was acquired).

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)

3. eBic Krios1 Movies

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

4637

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(1.047, 1.047)

Details:

contains unaligned movies corresponding to the data collection "eBic Krios1". The real pixel size is 1.047 Å/pix, and the dose rate is 1.003 e/Å^2/frame. Please use data/eBIC_Krios1_Movies/Gain_reference/gain.mrc as gain reference without any rotation or flipping.

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

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)

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

Structural basis for HIV-1 antagonism of host APOBEC3G via Cullin E3 ligase.

Ito F, Alvarez-Cabrera AL, Liu S, Yang H, Shiriaeva A, Zhou ZH, Chen XS. (2023)

The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection.

Rigden DJ, Fernández XM. (2023)

EMPIAR: the Electron Microscopy Public Image Archive.

Iudin A, Korir PK, Somasundharam S, Weyand S, Cattavitello C, Fonseca N, Salih O, Kleywegt GJ, Patwardhan A. (2023)

CLEMSite, a software for automated phenotypic screens using light microscopy and FIB-SEM.

Serra Lleti JM, Steyer AM, Schieber NL, Neumann B, Tischer C, Hilsenstein V, Holtstrom M, Unrau D, Kirmse R, Lucocq JM, Pepperkok R, Schwab Y. (2023)

Structure of a RecT/Redβ family recombinase in complex with a duplex intermediate of DNA annealing.

Caldwell BJ, Norris AS, Karbowski CF, Wiegand AM, Wysocki VH, Bell CE. (2022)

See all citations

Protein Data Bank Japan News

[2024-04-24]

354 new PDB entries have been released on 2024-04-24.

[2024-04-09]

[wwPDB] CASP16 Call for Targets

[2024-04-02]

Announcement of the PDBj Newsletter Vol.24 release

[2024-03-21]

[wwPDB] Paper Published on NMR Restraint Validation

[2024-03-13]

[wwPDB] Paper Published on CryoEM Archiving and Validation Recommendations

[2024-03-06]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

[2024-02-15]

Notice of Service Suspension (ASH, DASH, SeSAW, MAFFTash, Spanner, SFAS)

[2024-02-13]

[wwPDB] Biocurator Milestone: >10,000 Depositions Processed

[2024-02-06]

[wwPDB] Preprint Published on NMR Restraint Validation

[2024-02-05]

[wwPDB] Preprint Published on CryoEM Archiving and Validation Recommendations

See all news