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- EMDB-31473: Cryo-EM structure of SARS-CoV-2 spike in complex with two neutral... -

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Basic information

Entry
Database: EMDB / ID: EMD-31473
TitleCryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45
Map dataCryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45
Sample
  • Organelle or cellular component: Cryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 7.44 Å
AuthorsYang TJ / Yu PY / Wu HC / Hsu STD
Funding support Taiwan, 9 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-3114-Y-001-001 Taiwan
Academia Sinica (Taiwan)AS-CDA-109-L08 Taiwan
Academia Sinica (Taiwan)AS-CFII-108-110 Taiwan
Academia Sinica (Taiwan)AS-CFII108-111 Taiwan
Academia Sinica (Taiwan)AS-CFII-108-107 Taiwan
Academia Sinica (Taiwan)AS-SUMMIT-108 Taiwan
Academia Sinica (Taiwan)AS-CFII-108-102 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-3114-Y-001-002 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2823-8-001-001 Taiwan
CitationJournal: To Be Published
Title: Cryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45
Authors: Yang TJ / Yu PY / Wu HC / Hsu STD
History
DepositionJun 24, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31473.png

Downloads & links

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Map

FileDownload / File: emd_31473.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.58 Å/pix.
x 128 pix.
= 457.6 Å		3.58 Å/pix.
x 128 pix.
= 457.6 Å		3.58 Å/pix.
x 128 pix.
= 457.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.575 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.42 / Movie #1: 0.6
Minimum - Maximum-1.0502675 - 3.7557943
Average (Standard dev.)-0.00014255248 (±0.16960493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 457.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.5753.5753.575
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z457.600457.600457.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-1.0503.756-0.000

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of SARS-CoV-2 spike in complex with two neutral...

EntireName: Cryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45
Components
  • Organelle or cellular component: Cryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 spike in complex with two neutral...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 spike in complex with two neutralizing antibodies chAb-25 and chAb-45
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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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: 7.6
Component:
ConcentrationName
50.0 mMTris
150.0 mMNaCl
0.02 %sodium azide
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Details: generated by ab-initio reconstruction in cryoSPARC v2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27694
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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