- EMDB-26418: Asymmetric reconstruction of Tobacco mosaic virus (TMV) -
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Basic information
Entry
Database: EMDB / ID: EMD-26418
Title
Asymmetric reconstruction of Tobacco mosaic virus (TMV)
Map data
This is an ab initio reconstructed map. We don't have half maps but the journal is requiring us to deposit anyway. So I am upload three identical maps. Please let me know if this is allowed. Thanks.
Sample
Virus: Tobacco mosaic virus strain Dahlemense
Biological species
Tobacco mosaic virus strain Dahlemense
Method
single particle reconstruction / cryo EM / Resolution: 10.0 Å
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
U24GM116789
United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
R01AI111095
United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)
U01NS110437
United States
National Institutes of Health/National Institute on Aging (NIH/NIA)
RF1AG071177
United States
Citation
Journal: Sci Rep / Year: 2022 Title: Helical Indexing in Real Space. Authors: Chen Sun / Brenda Gonzalez / Wen Jiang / Abstract: Biological structures with helical symmetries of distinct twist, rise, and axial symmetry are abundant and span a wide range of organisms and functions. Performing de novo helical indexing remains ...Biological structures with helical symmetries of distinct twist, rise, and axial symmetry are abundant and span a wide range of organisms and functions. Performing de novo helical indexing remains challenging because of the steep learning curve involved in Fourier space layer lines. The unknown amount of out-of-plane tilt and the existence of multiple conformations of the helices further complicate indexing. In this work, we introduce a real-space indexing method that leverages the prior knowledge of the tilt and in-plane angles of the helical filaments/tubes, robust ab initio 3D reconstruction capabilities in single particle cryo-EM to obtain asymmetric reconstructions, and automatic indexing of helical parameters directly from the asymmetric density maps. We validated this approach using data from multiple helical structures of distinct helical symmetries, diameters, flexibility, data qualities, and heterogeneous states. The fully automated tool we introduce for real space indexing, HI3D, uses the 2D lattice in the autocorrelation of the cylindrical projection of a 3D density map to identify the helical symmetry. HI3D can often successfully determine the helical parameters of a suboptimal 3D density map, including ab initio single particle asymmetric reconstructions and sub-tomogram averages, with intermediate evidence that can also help assess the map quality. Furthermore, this open-source HI3D is usable independently as a Web application that can be accessed free of installation. With these methods, de novo helical indexing will be significantly more accessible to researchers investigating structures of helical filaments/tubes using cryo-EM.
Download / File: emd_26418.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
This is an ab initio reconstructed map. We don't have half maps but the journal is requiring us to deposit anyway. So I am upload three identical maps. Please let me know if this is allowed. Thanks.
Voxel size
X=Y=Z: 2.552 Å
Density
Contour Level
By AUTHOR: 0.0546
Minimum - Maximum
-0.117037684 - 0.1570664
Average (Standard dev.)
0.003255091 (±0.016820848)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
128
128
128
Spacing
128
128
128
Cell
A=B=C: 326.656 Å α=β=γ: 90.0 °
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Supplemental data
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Half map: This is an ab initio reconstructed map. We...
This is an ab initio reconstructed map. We don't have half maps but the journal is requiring us to deposit anyway. So I am upload three identical maps. Please let me know if this is allowed. Thanks.
This is an ab initio reconstructed map. We don't have half maps but the journal is requiring us to deposit anyway. So I am upload three identical maps. Please let me know if this is allowed. Thanks.
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Final angle assignment
Type: MAXIMUM LIKELIHOOD
Final reconstruction
Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Details: This is an ab initio map. No resolution / Number images used: 21744
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