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- EMDB-26418: Asymmetric reconstruction of Tobacco mosaic virus (TMV) -

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Basic information

Entry
Database: EMDB / ID: EMD-26418
TitleAsymmetric reconstruction of Tobacco mosaic virus (TMV)
Map dataThis 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 speciesTobacco mosaic virus strain Dahlemense
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsSun C / Gonzalez B / Jiang W
Funding support United States, 4 items
OrganizationGrant numberCountry
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
CitationJournal: 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.
History
DepositionMar 11, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJun 29, 2022-
Current statusJun 29, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_26418.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis 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 sizeX=Y=Z: 2.552 Å
Density
Contour LevelBy AUTHOR: 0.0546
Minimum - Maximum-0.117037684 - 0.1570664
Average (Standard dev.)0.003255091 (±0.016820848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=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...

Fileemd_26418_half_map_1.map
AnnotationThis 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.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: This is an ab initio reconstructed map. We...

Fileemd_26418_half_map_2.map
AnnotationThis 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.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Tobacco mosaic virus strain Dahlemense

EntireName: Tobacco mosaic virus strain Dahlemense
Components
  • Virus: Tobacco mosaic virus strain Dahlemense

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Supramolecule #1: Tobacco mosaic virus strain Dahlemense

SupramoleculeName: Tobacco mosaic virus strain Dahlemense / type: virus / ID: 1 / Parent: 0
Details: We generate this map by processing the EMPIAR 10305 dataset. We didn't collect this dataset.
NCBI-ID: 12246 / Sci species name: Tobacco mosaic virus strain Dahlemense / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.35000000000000003 µm / Nominal defocus min: 0.15 µm
Image recordingFilm 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 assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.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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