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- EMDB-45267: Open state SARS-COV2 spike protein from EMPIAR-10453 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45267
TitleOpen state SARS-COV2 spike protein from EMPIAR-10453
Map data
Sample
  • Virus: Severe acute respiratory syndrome coronavirus 2
Keywordsribosome / tomography / 70S
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 5.6 Å
AuthorsZhou Y / Huang QW / Bartesaghi A
Funding support United States, 1 items
OrganizationGrant numberCountry
Chan Zuckerberg InitiativeVisual Proteomics Imaging United States
CitationJournal: Nat Methods / Year: 2024
Title: MiLoPYP: self-supervised molecular pattern mining and particle localization in situ.
Authors: Qinwen Huang / Ye Zhou / Alberto Bartesaghi /
Abstract: Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to ...Cryo-electron tomography allows the routine visualization of cellular landscapes in three dimensions at nanometer-range resolutions. When combined with single-particle tomography, it is possible to obtain near-atomic resolution structures of frequently occurring macromolecules within their native environment. Two outstanding challenges associated with cryo-electron tomography/single-particle tomography are the automatic identification and localization of proteins, tasks that are hindered by the molecular crowding inside cells, imaging distortions characteristic of cryo-electron tomography tomograms and the sheer size of tomographic datasets. Current methods suffer from low accuracy, demand extensive and time-consuming manual labeling or are limited to the detection of specific types of proteins. Here, we present MiLoPYP, a two-step dataset-specific contrastive learning-based framework that enables fast molecular pattern mining followed by accurate protein localization. MiLoPYP's ability to effectively detect and localize a wide range of targets including globular and tubular complexes as well as large membrane proteins, will contribute to streamline and broaden the applicability of high-resolution workflows for in situ structure determination.
History
DepositionJun 8, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45267.png

Downloads & links

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Map

FileDownload / File: emd_45267.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 140 pix.
= 372.12 Å		2.66 Å/pix.
x 140 pix.
= 372.12 Å		2.66 Å/pix.
x 140 pix.
= 372.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.82
Minimum - Maximum-2.7831075 - 6.0058866
Average (Standard dev.)0.029787993 (±0.25260463)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 372.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45267_msk_1.map
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Half map: #1

Fileemd_45267_half_map_1.map
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Half map: #2

Fileemd_45267_half_map_2.map
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Sample components

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Entire : Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2
Components
  • Virus: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2697049
Sci species name: Severe acute respiratory syndrome coronavirus 2
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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 9194
ExtractionNumber tomograms: 266 / Number images used: 23388
Final angle assignmentType: MAXIMUM LIKELIHOOD

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