EMPIAR-10330 - 3.2 Å Single-Particle Cryo-EM Reconstruction of 49 kDa Membrane-Bound PfCRT Complexed with Fab [multiple data sets in MRCS and MRC formats]

EMPIAR-10330

3.2 Å Single-Particle Cryo-EM Reconstruction of 49 kDa Membrane-Bound PfCRT Complexed with Fab [multiple data sets in MRCS and MRC formats]

Publication:

Structure and drug resistance of the Plasmodium falciparum transporter PfCRT

Kim JK, Tan YZT, Wicht KJW, Erramilli SKE, Dhingra SKD, Okombo JO, Vendome JV, Hagenah LMH, Giacometti SIG, Warren ALW, Nosol KN, Roepe PDR, Potter CSP, Carragher BC, Kossiakoff AAK, Quick MQ, Fidock DAF, Mancia FM

Nature 576 (2019) 315-320

PMID: 31776516

DOI: 10.1038/s41586-019-1795-x

Related EMDB entry:

EMD-20806

Deposited:

2019-10-06

Released:

2019-12-19

Last modified:

2020-01-29

Imageset size:

830.42 GB

Imageset DOI:

10.6019/EMPIAR-10330

Experimental metadata:

Download xml json

Contains:

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

Image Sets

1. Unaligned and compressed multi-frame micrographs

Category:

micrographs - multiframe

Image format:

MRCS

No. of images or tilt series:

3383

Image size:

(3838, 3710)

Pixel type:

UNSIGNED 16 BIT INTEGER

Pixel spacing:

(0.5175, 0.5175)

Details:

Data collection was performed using a dose of ~91.56 e-/Å2 across 80 frames (75 msec per frame) at a dose rate of ~4.0 e–/pix/sec, using a set defocus range of -1.2 μm to -1.8 μm. Raw frames were compressed using pbzip2. Gain reference image to use is 18jun08i_08213559_01_3710x3838_norm_0_mod.mrc. Magnification anisotropy is present (Distortion angle of 172.7 degrees, major scale of 1.007 and minor scale of 0.993). The script to correct for magnification anisotropy (mag_distort_correct4.cs is attached, and it requires the mag_distortion_correct software available from the Grigorieff lab website.

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. Aligned and magnification anisotropy corrected micrographs

Category:

micrographs - single frame

Image format:

MRC

No. of images or tilt series:

3297

Image size:

(3838, 3710)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(0.5175, 0.5175)

Details:

Micrographs aligned using MotionCor2, magnification anisotropy corrected. Alignment was done initially using 3x3 patches (Patch3_micrographs). Micrographs that had estimated resolution at 0.5 confidence level of worse than 10 Å were removed, resulting in 3,297 micrographs. Patch2_micrographs were used later during refinement - hence only a subset of micrographs were aligned using 2x2 patches (Patch2_micrographs).

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. Final Particle Stack with Refined Euler Angles and Shifts

Category:

picked particles - single frame - processed

Image format:

MRC

No. of images or tilt series:

16905

Image size:

(300, 300)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(1.035, 1.035)

Details:

Final particle stack, with Relion .star file containing the refined Euler angles and shifts.

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

[2024-11-13]

236 new PDB entries have been released on 2024-11-13.

[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