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- EMDB-30461: cryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-30461
Titlecryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2
Map datacryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2
Sample
  • Complex: cryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2
    • Complex: SARS-CoV-2
    • Complex: T-ACE2
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsGuo L / Bi WW / Zhang YY / Yan RH / Li YN / Zhou Q / Dang BB
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: Cell Res / Year: 2021
Title: Engineered trimeric ACE2 binds viral spike protein and locks it in "Three-up" conformation to potently inhibit SARS-CoV-2 infection.
Authors: Liang Guo / Wenwen Bi / Xinling Wang / Wei Xu / Renhong Yan / Yuanyuan Zhang / Kai Zhao / Yaning Li / Mingfeng Zhang / Xia Cai / Shibo Jiang / Youhua Xie / Qiang Zhou / Lu Lu / Bobo Dang /
History
DepositionAug 18, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30461.png

Downloads & links

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Map

FileDownload / File: emd_30461.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å		1.09 Å/pix.
x 288 pix.
= 313.056 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.024599647 - 0.058376398
Average (Standard dev.)0.00013078243 (±0.0021956766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 313.056 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z313.056313.056313.056
α/β/γ90.00090.00090.000
start NX/NY/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0250.0580.000

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Supplemental data

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Sample components

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Entire : cryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2

EntireName: cryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2
Components
  • Complex: cryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2
    • Complex: SARS-CoV-2
    • Complex: T-ACE2

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Supramolecule #1: cryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2

SupramoleculeName: cryo EM map of the interface between RBD of SARS-CoV-2 and T-ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: SARS-CoV-2

SupramoleculeName: SARS-CoV-2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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Supramolecule #3: T-ACE2

SupramoleculeName: T-ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 59822
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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