EMPIAR-11848 - Cryo-EM of HCoV-NL63 5' proximal stem-loop 5 [multiple data sets in MRC format]

EMPIAR-11848

Cryo-EM of HCoV-NL63 5' proximal stem-loop 5 [multiple data sets in MRC format]

Publication:

Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses

Kretsch RC, Xu L, Zheludev IN, Zhou X, Huang R, Nye G, Li S, Zhang K, Chiu W, Das R

Proceedings of the National Academy of Sciences of the United States of America 121 (2024)

PMID: 38427602

DOI: 10.1073/pnas.2320493121

Related EMDB entry:

EMD-42813 EMD-42814

Deposited:

2023-11-28

Released:

2024-03-17

Last modified:

2024-03-17

Imageset size:

5.82 TB

Imageset DOI:

10.6019/EMPIAR-11848

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 (HCoV-NL63_SL5/exposures/*/FoilHole_*_Fractions.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:   10,884,517,904 kilobytes
Compressed size:  6,166,923,637 kilobytes

Contains:

micrographs - multiframe
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame micrographs of HCoV-NL63 5' stem-loop 5 RNA.

Category:

micrographs - multiframe

Image format:

MRC

No. of images or tilt series:

8304

Image size:

(4096, 4096)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(0.741, 0.741)

Details:

These micrographs were collected with a Titan Krios G3i, 300kV and a Falcon 4 detector with a Selectris energy filter with a 10eV slit. Over the collection, the sample was exposed evenly to 60 electrons per angstrom squared with a total exposure time of 3.61 seconds. Desired defocuses ranged from -1.2 to -2.0 nm. The exposures are gain corrected.

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 and orientations for final reconstruction of HCoV-NL63 5' stem-loop 5 RNA.

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

217720

Image size:

(230, 230)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.482, 1.482)

Details:

Particles extracted from motion-corrected micrographs. The orientations for the final reconstruction can be found in data/HCoV-NL63_SL5//particles/conformation*.cs for the two confromations.

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

[2020-07-15]

PDBj는 2020 년 7 월에 20 주년을 맞이했습니다.

[2019-02-20]

[wwPDB] 고분자결정구조 등록 시 PDBx/mmCIF 형식 파일만 허용됩니다.

[2017-11-16]

11 월 24 일 ~ 26 일, 텔레콤 센터 빌딩 (도쿄 오다이바)에서 개최되는 「사이언스 아고라 2017」에 출전합니다

[2016-01-28]

News on 2016-1-11

See all news