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- EMDB-30277: Cryo EM map of the interface between NTD of SARS-CoV-2 and 4A8 -

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Basic information

Entry
Database: EMDB / ID: EMD-30277
TitleCryo EM map of the interface between NTD of SARS-CoV-2 and 4A8
Map data
Sampleinterface between NTD of SARS-CoV-2 and 4A8
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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.
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: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30277.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: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07347295 - 0.124248266
Average (Standard dev.)0.0002534746 (±0.0023612755)
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/NZ777686
NX/NY/NZ10710993
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0730.1240.000

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Supplemental data

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Sample components

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Entire interface between NTD of SARS-CoV-2 and 4A8

EntireName: interface between NTD of SARS-CoV-2 and 4A8 / Number of components: 1

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Component #1: protein, interface between NTD of SARS-CoV-2 and 4A8

ProteinName: interface between NTD of SARS-CoV-2 and 4A8 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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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: 217743
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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