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- EMDB-30276: cryo EM map of the S protein of SARS-CoV-2 in complex bound with 4A8 -

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Basic information

Entry
Database: EMDB / ID: EMD-30276
Titlecryo EM map of the S protein of SARS-CoV-2 in complex bound with 4A8
Map data
SampleS protein of SARS-CoV-2 in complex bound with 4A8:
Spike glycoprotein / heavy chain of 4A8 / light chain of 4A8 / ligand
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell surface receptor binding / viral entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / pathogenesis / host cell plasma membrane / virion membrane / integral component of membrane
Spike glycoprotein S2, coronavirus / Spike receptor binding domain, betacoronavirus / Spike glycoprotein, heptad repeat 2, coronavirus / Spike receptor binding domain superfamily, coronavirus
Spike glycoprotein
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYan RH / Zhang YY / Guo YY / Li YN / Xia L / Zhou Q
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: Science / Year: 2020
Title: A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2.
Authors: Xiangyang Chi / Renhong Yan / Jun Zhang / Guanying Zhang / Yuanyuan Zhang / Meng Hao / Zhe Zhang / Pengfei Fan / Yunzhu Dong / Yilong Yang / Zhengshan Chen / Yingying Guo / Jinlong Zhang / ...Authors: Xiangyang Chi / Renhong Yan / Jun Zhang / Guanying Zhang / Yuanyuan Zhang / Meng Hao / Zhe Zhang / Pengfei Fan / Yunzhu Dong / Yilong Yang / Zhengshan Chen / Yingying Guo / Jinlong Zhang / Yaning Li / Xiaohong Song / Yi Chen / Lu Xia / Ling Fu / Lihua Hou / Junjie Xu / Changming Yu / Jianmin Li / Qiang Zhou / Wei Chen /
Abstract: Developing therapeutics against SARS-CoV-2 could be guided by the distribution of epitopes, not only on the receptor binding domain (RBD) of the Spike (S) protein, but also across the full Spike (S) ...Developing therapeutics against SARS-CoV-2 could be guided by the distribution of epitopes, not only on the receptor binding domain (RBD) of the Spike (S) protein, but also across the full Spike (S) protein. We isolated and characterized monoclonal antibodies (mAbs) from ten convalescent COVID-19 patients. Three mAbs showed neutralizing activities against authentic SARS-CoV-2. An mAb, named 4A8, exhibits high neutralization potency against both authentic and pseudotyped SARS-CoV-2, but does not bind the RBD. We defined the epitope of 4A8 as the N terminal domain (NTD) of the S protein by determining its cryo-EM structure in complex with the S protein to an overall resolution of 3.1 Angstrom and local resolution of 3.3 Angstrom for the 4A8-NTD interface. This points to the NTD as a promising target for therapeutic mAbs against COVID-19.
Validation ReportPDB-ID: 7c2l

SummaryFull reportAbout validation report
History
DepositionMay 8, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 8, 2020-
Current statusJul 8, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7c2l
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30276.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.017
Minimum - Maximum-0.075862505 - 0.14391066
Average (Standard dev.)0.00020944767 (±0.0044085)
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-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0760.1440.000

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Supplemental data

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Sample components

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Entire S protein of SARS-CoV-2 in complex bound with 4A8

EntireName: S protein of SARS-CoV-2 in complex bound with 4A8 / Number of components: 5

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Component #1: protein, S protein of SARS-CoV-2 in complex bound with 4A8

ProteinName: S protein of SARS-CoV-2 in complex bound with 4A8 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Spike glycoprotein

ProteinName: Spike glycoprotein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 142.502594 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, heavy chain of 4A8

ProteinName: heavy chain of 4A8 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 50.097188 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, light chain of 4A8

ProteinName: light chain of 4A8 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.02075 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 89 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 171673
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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