EMPIAR-12002 - Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the apo state from Krios microscope [multiple data sets in TIFF and MRC formats]

EMPIAR-12002

Single-particle cryo-EM dataset of the glycosyltransferase ArnC from Salmonella enterica in the apo state from Krios microscope [multiple data sets in TIFF and MRC formats]

Publication:

Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria

Ashraf KU, Bunoro-Batista M, Ansell TB, Punetha A, Rosario-Garrido S, Firlar E, Kaelber JT, Stansfeld PJ, Petrou VI

bioRxiv (2025)

DOI: 10.1101/2025.01.29.634835

Related EMDB entry:

EMD-44302

Deposited:

2024-03-05

Released:

2025-06-02

Last modified:

2025-06-02

Imageset size:

5.92 TB

Imageset DOI:

10.6019/EMPIAR-12002

Experimental metadata:

Download xml json

Contains:

micrographs - multiframe
micrographs - single frame
picked particles - single frame - processed

Image Sets

1. Unaligned multi-frame micrographs of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - "Elizabeth"

Category:

micrographs - multiframe

Image format:

TIFF

No. of images or tilt series:

23259

Image size:

(5760, 4092)

Pixel type:

UNSIGNED BYTE

Pixel spacing:

(0.646, 0.646)

Details:

The dataset contains unaligned non gain-corrected micrograph movies in TIFF format. Cryo-EM data were collected at the National Center for Cryo-EM Access and Training (NCCAT) using the 300kV Titan Krios #4 – “Elizabeth” (TFS) electron microscope, equipped with a K3 direct electron detector (Gatan) and a BioQuantum energy filter (Gatan) with slit width of 20 eV. Data were collected automatically in counting mode using image shift in Leginon, a nominal magnification of 130,000X, a nominal pixel size of 0.646 Å/pixel, and a dose rate of 19.9685 electrons/pixel/s. Movies were recorded at 30 ms/frame for 1.2s (40 frames total), resulting in a total dose of 57.42 electrons/Å2. Nominal defocus range was -0.8 to -2.0 μm. A total of 23,259 micrographs were recorded from one grid over three days. Micrographs were not gain-normalized or defect corrected. The gain reference is the file named "n21sep13b*norm_0.mrc" in the "references" folder. When importing into cryoSPARC the gain reference should be flipped in the Y axis. At the end of processing a calibrated pixel size of 0.67 Å/pixel was determined for this dataset, representing an 3.72% error from the nominal pixel size value.

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. Aligned and dose-weighted micrographs of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - "Elizabeth"

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

16451

Image size:

(5760, 4092)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.646, 0.646)

Details:

Aligned and dose-weighted micrographs produced from the raw movies using patch motion correction in cryoSPARC. The dataset contains a subset of micrographs that have contributed particles to the final particle stack. Nominal pixel size 0.646 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.67 Å/pixel.

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. Final particle stack of ArnC from S. enterica in the apo state collected on NCCAT Titan Krios #4 - "Elizabeth"

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

16451

Image size:

(480, 480)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.646, 0.646)

Details:

Final particle stack of 490,807 particles from 16,451 aligned/dose-weighted micrographs corresponding to the reconstruction deposited in EMD-44302. Nominal pixel size 0.646 Å/pixel. Calibrated pixel size imposed on final reconstruction is 0.67 Å/pixel. Box size of 480 px was used.

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

[2025-06-04]

343 new PDB entries have been released on 2025-06-04.

[2025-04-18]

[wwPDB] Download Snapshots of the PDB Core Archive via HTTPS, SYNC, RSYNC, or FTP

[2025-03-25]

Announcement of the PDBj Newsletter Vol.25 release

[2025-03-11]

[wwPDB] Poster Prize Awarded at The Biophysical Society Meeting

[2025-03-10]

[wwPDB] New version of PDB-IHM validation reports now include assessments of crosslinking mass spectrometry-based structure models