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- EMDB-43869: HIV-1 capsid-SP1 subtomogram averaging obtained from EMPIAR-10164... -

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Basic information

Entry
Database: EMDB / ID: EMD-43869
TitleHIV-1 capsid-SP1 subtomogram averaging obtained from EMPIAR-10164 using TomoNet and Relion4 (4 tilt-series)
Map datafull map
Sample
  • Complex: Human immunodeficiency virus 1Subtypes of HIV
KeywordsHIV-1 capsid-SP1 / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 3.2 Å
AuthorsWang H / Zhou ZH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
CitationJournal: Biol Imaging / Year: 2024
Title: TomoNet: A streamlined cryogenic electron tomography software pipeline with automatic particle picking on flexible lattices.
Authors: Hui Wang / Shiqing Liao / Xinye Yu / Jiayan Zhang / Z Hong Zhou /
Abstract: Cryogenic electron tomography (cryoET) is capable of determining biological structures of molecular complexes at near-atomic resolution by averaging half a million subtomograms. While abundant ...Cryogenic electron tomography (cryoET) is capable of determining biological structures of molecular complexes at near-atomic resolution by averaging half a million subtomograms. While abundant complexes/particles are often clustered in arrays, precisely locating and seamlessly averaging such particles across many tomograms present major challenges. Here, we developed TomoNet, a software package with a modern graphical user interface to carry out the entire pipeline of cryoET and subtomogram averaging to achieve high resolution. TomoNet features built-in automatic particle picking and three-dimensional (3D) classification functions and integrates commonly used packages to streamline high-resolution subtomogram averaging for structures in 1D, 2D, or 3D arrays. Automatic particle picking is accomplished in two complementary ways: one based on template matching and the other using deep learning. TomoNet's hierarchical file organization and visual display facilitate efficient data management as required for large cryoET datasets. Applications of TomoNet to three types of datasets demonstrate its capability of efficient and accurate particle picking on flexible and imperfect lattices to obtain high-resolution 3D biological structures: virus-like particles, bacterial surface layers within cellular lamellae, and membranes decorated with nuclear egress protein complexes. These results demonstrate TomoNet's potential for broad applications to various cryoET projects targeting high-resolution structures.
History
DepositionFeb 28, 2024-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43869.png

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Map

FileDownload / File: emd_43869.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 192 pix.
= 259.2 Å		1.35 Å/pix.
x 192 pix.
= 259.2 Å		1.35 Å/pix.
x 192 pix.
= 259.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
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Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-1.9928899 - 3.6317403
Average (Standard dev.)0.000000000002002 (±0.2802295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43869_msk_1.map
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Half map: half map 1

Fileemd_43869_half_map_1.map
Annotationhalf map 1
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Half map: half map 2

Fileemd_43869_half_map_2.map
Annotationhalf map 2
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Sample components

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Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Complex: Human immunodeficiency virus 1Subtypes of HIV

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: NITROGEN

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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: 5.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Number real images: 41 / Average electron dose: 90.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 4 / Number images used: 13558
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Details: We used Relion4 for the final alignment / Number subtomograms used: 13558
FSC plot (resolution estimation)

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