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- EMDB-11833: cryo-EM map of the trimeric Spike-ACE2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-11833
Titlecryo-EM map of the trimeric Spike-ACE2 complex
Map dataSpike-ACE2 complex trimer
Sample
  • Complex: SARS-COV2 Spike-ACE trimeric complex
    • Complex: SARS-COV2 Spike
    • Complex: ACE
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Cricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsDong CN
CitationJournal: To Be Published
Title: Structural investigation of ACE2 dependent disassembly of the trimeric SARS-CoV-2 Spike glycoprotein
Authors: Dong CN / Henning S
History
DepositionOct 12, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateOct 28, 2020-
Current statusOct 28, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11833.png

Downloads & links

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Map

FileDownload / File: emd_11833.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSpike-ACE2 complex trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 280 pix.
= 369.012 Å		1.32 Å/pix.
x 280 pix.
= 369.012 Å		1.32 Å/pix.
x 280 pix.
= 369.012 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3179 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.08
Minimum - Maximum-0.5597603 - 1.5627884
Average (Standard dev.)0.000225467 (±0.05722271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 369.012 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31791.31791.3179
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z369.012369.012369.012
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.5601.5630.000

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Supplemental data

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Additional map: Spike-ACE2 complex trimer low pass

Fileemd_11833_additional_1.map
AnnotationSpike-ACE2 complex trimer low pass
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-COV2 Spike-ACE trimeric complex

EntireName: SARS-COV2 Spike-ACE trimeric complex
Components
  • Complex: SARS-COV2 Spike-ACE trimeric complex
    • Complex: SARS-COV2 Spike
    • Complex: ACE

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Supramolecule #1: SARS-COV2 Spike-ACE trimeric complex

SupramoleculeName: SARS-COV2 Spike-ACE trimeric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: SARS-COV2 Spike

SupramoleculeName: SARS-COV2 Spike / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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Supramolecule #3: ACE

SupramoleculeName: ACE / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)

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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: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 300.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 75.0 µm / Calibrated defocus max: 0.0025 µm / Calibrated defocus min: 0.0008 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47901
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: COMMON LINE

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