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- EMDB-34873: S protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-34873
TitleS protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 sub-complex
Map data
Sample
  • Complex: S protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 sub-complex
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhang YY / Guo YY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971123 China
CitationJournal: MedComm (2020) / Year: 2024
Title: Defining the features and structure of neutralizing antibody targeting the silent face of the SARS-CoV-2 spike N-terminal domain.
Authors: Zhaoyong Zhang / Yuanyuan Zhang / Yuting Zhang / Linling Cheng / Lu Zhang / Qihong Yan / Xuesong Liu / Jiantao Chen / Jun Dai / Yingying Guo / Peilan Wei / Xinyi Xiong / Juxue Xiao / Airu ...Authors: Zhaoyong Zhang / Yuanyuan Zhang / Yuting Zhang / Linling Cheng / Lu Zhang / Qihong Yan / Xuesong Liu / Jiantao Chen / Jun Dai / Yingying Guo / Peilan Wei / Xinyi Xiong / Juxue Xiao / Airu Zhu / Jianfen Zhuo / Ruoxi Cai / Jingjun Zhang / Haiyue Rao / Bin Qu / Shengnan Zhang / Jiaxin Feng / Jinling Cheng / Jingyi Su / Canjie Chen / Shu Li / Yuanyuan Zhang / Lei Chen / Yingkang Jin / Yonghao Xu / Xiaoqing Liu / Yimin Li / Jingxian Zhao / Yanqun Wang / Qiang Zhou / Jincun Zhao /
Abstract: Research on virus/receptor interactions has uncovered various mechanisms of antibody-mediated neutralization against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ...Research on virus/receptor interactions has uncovered various mechanisms of antibody-mediated neutralization against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, understanding of neutralization by antibodies targeting the silent face, which recognize epitopes on glycan shields, remains limited, and their potential protective efficacy in vivo is not well understood. This study describes a silent face neutralizing antibody, 3711, which targets a non-supersite on the N-terminal domain (NTD) of the spike protein. Cryo-EM structure determination of the 3711 Fab in the spike complex reveals a novel neutralizing epitope shielded by glycans on the spike's silent face. Antibody 3711 inhibits the interaction between the receptor-binding domain (RBD) and human angiotensin-converting enzyme 2 (hACE2) through steric hindrance and exhibits superior in vivo protective effects compared to other reported NTD-targeted monoclonal antibodies (mAbs). Competition assays and antibody repertoire analysis indicate the rarity of antibodies targeting the 3711-related epitope in SARS-CoV-2 convalescents, suggesting the infrequency of NTD silent face-targeted neutralizing antibodies during SARS-CoV-2 infection. As the first NTD silent face-targeted neutralizing antibody against SARS-CoV-2, the identification of mAb 3711, with its novel neutralizing mechanism, enhances our understanding of neutralizing epitopes on glycan shields and elucidates epitope-guided viral mutations that evade specific antibodies.
History
DepositionNov 29, 2022-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34873.png

Downloads & links

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Map

FileDownload / File: emd_34873.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.11055336 - 0.16803357
Average (Standard dev.)0.00010654919 (±0.002995199)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #1

Fileemd_34873_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_34873_half_map_2.map
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Sample components

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Entire : S protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 ...

EntireName: S protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 sub-complex
Components
  • Complex: S protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 sub-complex

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Supramolecule #1: S protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 ...

SupramoleculeName: S protein of SARS-CoV-2 in complex with 3711 focused on NTD_3711 sub-complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: 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: 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 176801
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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