EMPIAR logo

Electron Microscopy Public Image Archive

EMPIAR-10202
Sub-2 Å Single-Particle Cryo-EM Reconstruction of AAV2-L336C [multiple data sets in MRC and MRCS formats]
Publication:

Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant

Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D

Nature communications 9 (2018)

PMID: 30194371

Related EMDB entry:
EMD-9012
Deposited:
2018-07-28
Released:
2018-08-08
Last modified:
2019-06-07
Imageset size:
5.67 TB
Imageset DOI:
10.6019/EMPIAR-10202
Experimental metadata:
Download xml json
Contains:
  • micrographs - multiframe
  • micrographs - single frame
Image Sets
1. Unaligned, compressed, raw movie frames of AAV2-L336C
Category:
micrographs - multiframe
Image format:
MRC
No. of images or tilt series:
1317
Image size:
(7420, 7676)
Pixel type:
SIGNED BYTE
Pixel spacing:
(0.394, 0.394)
Details:
Unaligned, compressed, raw movie frames of AAV2-L336C. The gain normalization reference images (norm) are included. No dark gain reference images are present because dark images values are always zero in counting mode camera. Magnification anisotropy measured using gold diffraction was found to be 1.005 at major axis, 0.995 at minor axis, at 7.7 degrees angle. Total dose was 22.5 electrons per Å squared over 3.5 seconds. Calibrated pixel size is 0.394 Å/pixel.
Files:
Loading...
2. MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2 movie frames of AAV2-L336C
Category:
micrographs - multiframe
Image format:
MRC
No. of images or tilt series:
1317
Image size:
(3710, 3838)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(0.788, 0.788)
Details:
MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2 movie frames of AAV2-L336C. Movie frames were aligned using MotionCor2 with 5 by 5 patches, a grouping of 3 and B-factor of 100, and Fourier space binning of 2 (resulting in a pixel size of 0.788 Å/pixel) through the Appion software package. No dose weighting was applied for these movies frames.
Files:
Loading...
3. MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2, dose weighted, summed micrographs of AAV2-L336C
Category:
micrographs - single frame
Image format:
MRC
No. of images or tilt series:
1317
Image size:
(3710, 3838)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(0.788, 0.788)
Details:
MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2 movie frames of AAV2-L336C. Movie frames were aligned using MotionCor2 with 5 by 5 patches, a grouping of 3 and B-factor of 100, and Fourier space binning of 2 (resulting in a pixel size of 0.788 Å/pixel) through the Appion software package. Dose weighting was applied for these summed micrographs, using a dose per frame of 0.3214 electrons per Å squared.
Files:
Loading...
4. MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2, not dose weighted, summed micrographs of AAV2-L336C
Category:
micrographs - single frame
Image format:
MRC
No. of images or tilt series:
1317
Image size:
(3710, 3838)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(0.788, 0.788)
Details:
MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2 movie frames of AAV2-L336C. Movie frames were aligned using MotionCor2 with 5 by 5 patches, a grouping of 3 and B-factor of 100, and Fourier space binning of 2 (resulting in a pixel size of 0.788 Å/pixel) through the Appion software package. These are the non-dose weighted summed micrographs that can be used for CTF estimation.
Files:
Loading...
5. MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2, not dose weighted, frames 5 to 19 summed micrographs of AAV2-L336C
Category:
micrographs - single frame
Image format:
MRC
No. of images or tilt series:
1317
Image size:
(3710, 3838)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(0.788, 0.788)
Details:
MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2 movie frames of AAV2-L336C. Movie frames were aligned using MotionCor2 with 5 by 5 patches, a grouping of 3 and B-factor of 100, and Fourier space binning of 2 (resulting in a pixel size of 0.788 Å/pixel) through the Appion software package. Frames 5 to 19 were summed and no dose weighting was applied, as these corresponded to frames that gave the best resolution reconstructions individually compared to the other frames. Note that the signal-to-noise ratio in these micrographs are less those from all 70 frames, and should only be used for the final refinements and reconstructions once Euler angles and shifts have been established.
Files:
Loading...
6. Final particle stack of AAV2-L336C using frames 5 to 19
Category:
micrographs - single frame
Image format:
MRCS
No. of images or tilt series:
30515
Image size:
(800, 800)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(0.788, 0.788)
Details:
Final set of AAV2-L336C particles extracted from MotionCor2 aligned, gain corrected, magnification anisotropy corrected, Fourier bin by 2, not dose weighted, frames 5 to 19 summed micrographs. A Relion .star format file is provided and contains the final Euler angles, shifts and also the micrograph coordinates.
Files:
Loading...
7. Final particle stack of AAV2-L336C grouped into frames 5-9, 10-14 and 15-19, after rotational alignment
Category:
micrographs - single frame
Image format:
MRC
No. of images or tilt series:
91545
Image size:
(800, 800)
Pixel type:
32 BIT FLOAT
Pixel spacing:
(0.788, 0.788)
Details:
From the final set of 30515 particles, each particle was expanded into 3: a particle for frames 5-9, one for frames 10-14 and one for frames 15-19. This resulted in a stack 3 times larger that was used for rotational alignment in Frealign. A .mrc stack and Frealign .par file are provided with the final Euler angles and shifts.
Files:
Loading...
Browse All Files
Files:
Loading...
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
Contact us
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
[2024-11-01]
A new portal integrating genome variants and protein structures has released
[2024-10-30]
294 new PDB entries have been released on 2024-10-30.
[2024-10-25]
PDBj luncheon seminar at APBJC 2024
[2024-10-17]
[wwPDB] The Nobel Prize in Chemistry 2024
[2024-10-16]
[wwPDB] wwPDB Data Release Policy on Public Preprint Archives
[2024-10-09]
[wwPDB] Annotation of Protein Modifications in the PDB
[2024-10-03]
[wwPDB] Access IHM structures at wwPDB DOI Landing Pages
[2024-09-18]
[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024
[2024-09-12]
[wwPDB] Paper Published on CryoEM Archiving and Validation Recommendations
[2024-09-11]
[wwPDB] PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)
See all news