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- EMDB-16209: HIV-1 CA-SP1 subtomogram average with Relion4 from EMPIAR-10164 d... -

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Basic information

Entry
Database: EMDB / ID: EMD-16209
TitleHIV-1 CA-SP1 subtomogram average with Relion4 from EMPIAR-10164 dataset, 3.0 A from the full dataset
Map dataHIV-1 CA-SP1 subtomogram average, from the full dataset, relion4.0 tomo
Sample
  • Virus: Human immunodeficiency virus 1
KeywordsHIV-1 CA-SP1 / data from EMPIAR-10164 / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 3.0 Å
AuthorsKe Z / Briggs JAG / Scheres SHW
Funding support United Kingdom, European Union, Germany, 5 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC UP A025 1013 United Kingdom
UK Research and Innovation (UKRI)MC UP 1201/ United Kingdom
European Research Council (ERC)ERCCoG- 2014European Union
European Research Council (ERC)ERC StG-2019European Union
Max Planck SocietyJ.A.G.B. Germany
CitationJournal: Elife / Year: 2022
Title: A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0.
Authors: Jasenko Zivanov / Joaquín Otón / Zunlong Ke / Andriko von Kügelgen / Euan Pyle / Kun Qu / Dustin Morado / Daniel Castaño-Díez / Giulia Zanetti / Tanmay A M Bharat / John A G Briggs / Sjors H W Scheres /
Abstract: We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are ...We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, particularly for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.
History
DepositionNov 22, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16209.png

Downloads & links

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Map

FileDownload / File: emd_16209.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 CA-SP1 subtomogram average, from the full dataset, relion4.0 tomo
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: 0.08
Minimum - Maximum-0.35316357 - 0.64566797
Average (Standard dev.)0.0014036638 (±0.016034275)
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_16209_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 CA-SP1 subtomogram average, from the full dataset,...

Fileemd_16209_half_map_1.map
AnnotationHIV-1 CA-SP1 subtomogram average, from the full dataset, relion4.0 tomo, half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: HIV-1 CA-SP1 subtomogram average, from the full dataset,...

Fileemd_16209_half_map_2.map
AnnotationHIV-1 CA-SP1 subtomogram average, from the full dataset, relion4.0 tomo, half2 map
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
Details: HIV-1 dMACANC virus-like particles assembled in the presence of BVM.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes
Molecular weightTheoretical: 74 KDa

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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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Software - details: Relion4 tomo / Number subtomograms used: 144275
ExtractionNumber tomograms: 43 / Number images used: 144275
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) / Software - details: Relion4 tomo / Details: Relion-4.0 software
FSC plot (resolution estimation)

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