EMPIAR-10675 - The Myosin II Coiled Coil Domain Atomic Structure in its Native Environment [multiple data sets in MRC and MRCS formats]

EMPIAR-10675

The Myosin II Coiled Coil Domain Atomic Structure in its Native Environment [multiple data sets in MRC and MRCS formats]

Publication:

The myosin II coiled-coil domain atomic structure in its native environment

Rahmani H, Ma W, Hu Z, Daneshparvar N, Taylor DW, McCammon JA, Irving TC, Edwards RJ, Taylor KA

Proceedings of the National Academy of Sciences of the United States of America 118 (2021)

PMID: 33782130

DOI: 10.1073/pnas.2024151118

Related EMDB entry:

EMD-22975

Deposited:

2019-11-04

Released:

2021-07-29

Last modified:

2022-02-28

Imageset size:

13.30 TB

Imageset DOI:

10.6019/EMPIAR-10675

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 (Frames*/*/rawdata/*frames.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:   16,376,925,619 bytes
Compressed size: 10,465,372,567 bytes

Contains:

micrographs - multiframe
micrographs - single frame
picked particles - single frame - unprocessed

Image Sets

1. Frame Stacks 1/3

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

1432

Image size:

(8192, 8192)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.009, 1.009)

Details:

Particle positions are given in the final star file in the particle stack directory.

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. Frame Stacks 2/3

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

591

Image size:

(8192, 8192)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.009, 1.009)

Details:

---

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. Frame Stacks 3/3

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

1432

Image size:

(8192, 8192)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.009, 1.009)

Details:

---

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)

4. Micrographs before frames alignment

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

3507

Image size:

(8192, 8192)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.009, 1.009)

Details:

Micrographs before frame alignment.
Gain References to be used for frame alignment are stored in
data/Micrographs/17dec15_ref_a

directory.

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)

5. Micrographs: frame-aligned and dose-weighted

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

3507

Image size:

(8192, 8192)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.009, 1.009)

Details:

---

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)

6. Particle Stack

Category:

picked particles - single frame - unprocessed

Image format:

MRCS

No. of images or tilt series:

216045

Image size:

(768, 768)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.009, 1.009)

Details:

Particle stack produced using relion with .star and .mrcs files. The mrcs file has been split with the command:
split -b 10000000k 17dec15a-768-localctf.mrcs -d parts-

To combine it back execute:
cat parts-* > 17dec15a-768-localctf_combined.mrcs

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

Browse EMPIAR

Sample Preparation Widget

Volume Browser

Tomo Viewer Prototype

Claim entries to your ORCiD

Talks and Tutorials

EMPIAR Quick tour

Publications

Re-use study

Statistics

EMPIAR in the news

COVID-19 Data Portal

EMDB

BioImage Archive

PDBe

EMNavigator@PDBj

PDBj

Citations

prismPYP: Power-spectrum and image domain learning for self-supervised micrograph evaluation.

He L, Bartesaghi A. (2026)

CryoSIP: unleashing protein high-resolution Cryo-EM via semantic-instance collaborative picking.

Deng Y, Wang S, Xiang M, Li Y, Zhuo L, Cao D, Fu X, Zou Q. (2026)

Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.

Fonseca N, Duraisamy AK, Wang Z, Somasundharam S, Tayebinia M, de Oliveira LC, Ma M, Turner J, Patwardhan A, Kleywegt GJ, Hartley M, Morris KL. (2026)

CryoVirusDB: An Annotated Dataset for AI-Based Virus Particle Identification in Cryo-EM Micrographs.

Gyawali R, Dhakal A, Wang L, Cheng J. (2026)

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements.

Jones HN, Deshmukh A, Pande K. (2026)

CryoGS: High-Quality Cryo-EM Homogeneous Reconstruction by Gaussian Splatting

Zeng B, Liu S, Cheng S, Xu G, Fan H. (2026)

Point cloud deformation modeling for particle selection following cryo-EM 2D classification.

Wang X, Mo Z, Li F, Zhang F, Wan X. (2026)

ICECREAM: high-fidelity equivariant cryo-electron tomography.

Kishore V, Debarnot V, Righetto RD, Engel BD, Dokmanić I. (2026)

CryoSift: an accessible and automated CNN-driven tool for cryo-EM 2D class selection.

Schäfer JH, Calza A, Hom K, Damodar P, Peng R, Bogdanović N, Lander GC, Stagg SM, Cianfrocco MA. (2025)