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- EMDB-50672: A 3.3A sub-tomogram average of HIV-1 CA-SP1 from 5 tomograms in E... -

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Basic information

Entry
Database: EMDB / ID: EMD-50672
TitleA 3.3A sub-tomogram average of HIV-1 CA-SP1 from 5 tomograms in EMPIAR-10164 obtained using RELION 5
Map dataUnmasked map after running the final 'Post-processing' job in RELION 5.
Sample
  • Virus: Human immunodeficiency virus 1
Keywordsvirus-like particle / enveloped / empty / VIRUS
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 3.3 Å
AuthorsToader B / Scheres SHW
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1013 United Kingdom
Citation
Journal: FEBS Open Bio / Year: 2024
Title: An image processing pipeline for electron cryo-tomography in RELION-5.
Authors: Alister Burt / Bogdan Toader / Rangana Warshamanage / Andriko von Kügelgen / Euan Pyle / Jasenko Zivanov / Dari Kimanius / Tanmay A M Bharat / Sjors H W Scheres /
Abstract: Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be ...Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution for de novo atomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and interoperability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION-5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for interoperability with other software tools and provides a framework for further standardisation.
#1: Journal: Biorxiv / Year: 2024
Title: An image processing pipeline for electron cryo-tomography in RELION-5
Authors: Burt A / Toader B / Warshamanage R / von Kugelgen A / Pyle E / Zivanov J / Kimanius D / Bharat T / Scheres S
History
DepositionJun 17, 2024-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50672.png

Downloads & links

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Map

FileDownload / File: emd_50672.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnmasked map after running the final 'Post-processing' job in RELION 5.
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.89
Minimum - Maximum-5.142007 - 7.8236
Average (Standard dev.)-0.00000000000776 (±0.5653958)
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_50672_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map from the final 'Reconstruct particle' job in RELION 5.

Fileemd_50672_half_map_1.map
AnnotationHalf-map from the final 'Reconstruct particle' job in RELION 5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map from the final 'Reconstruct particle' job in RELION 5.

Fileemd_50672_half_map_2.map
AnnotationHalf-map from the final 'Reconstruct particle' job in RELION 5.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1

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Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 9038
ExtractionNumber tomograms: 5 / Number images used: 36088 / Software - Name: RELION (ver. 5.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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