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- EMDB-31642: Local construction of SARS-CoV-2 S protein RBD in complex with XG... -

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Basic information

Entry
Database: EMDB / ID: EMD-31642
TitleLocal construction of SARS-CoV-2 S protein RBD in complex with XG014 Fab
Map data
Sample
  • Complex: XG014 in complex with S trimer of SARS-CoV-2
    • Complex: S trimer of SARS-CoV-2
    • Complex: XG014 Fab
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang K / Wang XX
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesYSBR-010 China
CitationJournal: Protein Cell / Year: 2022
Title: An ultrapotent pan-β-coronavirus lineage B (β-CoV-B) neutralizing antibody locks the receptor-binding domain in closed conformation by targeting its conserved epitope.
Authors: Zezhong Liu / Wei Xu / Zhenguo Chen / Wangjun Fu / Wuqiang Zhan / Yidan Gao / Jie Zhou / Yunjiao Zhou / Jianbo Wu / Qian Wang / Xiang Zhang / Aihua Hao / Wei Wu / Qianqian Zhang / Yaming Li ...Authors: Zezhong Liu / Wei Xu / Zhenguo Chen / Wangjun Fu / Wuqiang Zhan / Yidan Gao / Jie Zhou / Yunjiao Zhou / Jianbo Wu / Qian Wang / Xiang Zhang / Aihua Hao / Wei Wu / Qianqian Zhang / Yaming Li / Kaiyue Fan / Ruihong Chen / Qiaochu Jiang / Christian T Mayer / Till Schoofs / Youhua Xie / Shibo Jiang / Yumei Wen / Zhenghong Yuan / Kang Wang / Lu Lu / Lei Sun / Qiao Wang /
Abstract: New threats posed by the emerging circulating variants of SARS-CoV-2 highlight the need to find conserved neutralizing epitopes for therapeutic antibodies and efficient vaccine design. Here, we ...New threats posed by the emerging circulating variants of SARS-CoV-2 highlight the need to find conserved neutralizing epitopes for therapeutic antibodies and efficient vaccine design. Here, we identified a receptor-binding domain (RBD)-binding antibody, XG014, which potently neutralizes β-coronavirus lineage B (β-CoV-B), including SARS-CoV-2, its circulating variants, SARS-CoV and bat SARSr-CoV WIV1. Interestingly, antibody family members competing with XG014 binding show reduced levels of cross-reactivity and induce antibody-dependent SARS-CoV-2 spike (S) protein-mediated cell-cell fusion, suggesting a unique mode of recognition by XG014. Structural analyses reveal that XG014 recognizes a conserved epitope outside the ACE2 binding site and completely locks RBD in the non-functional "down" conformation, while its family member XG005 directly competes with ACE2 binding and position the RBD "up". Single administration of XG014 is effective in protection against and therapy of SARS-CoV-2 infection in vivo. Our findings suggest the potential to develop XG014 as pan-β-CoV-B therapeutics and the importance of the XG014 conserved antigenic epitope for designing broadly protective vaccines against β-CoV-B and newly emerging SARS-CoV-2 variants of concern.
History
DepositionAug 8, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJul 6, 2022-
Current statusJul 6, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31642.png

Downloads & links

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Map

FileDownload / File: emd_31642.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.07582625 - 0.118993744
Average (Standard dev.)1.9392002e-05 (±0.0008550252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : XG014 in complex with S trimer of SARS-CoV-2

EntireName: XG014 in complex with S trimer of SARS-CoV-2
Components
  • Complex: XG014 in complex with S trimer of SARS-CoV-2
    • Complex: S trimer of SARS-CoV-2
    • Complex: XG014 Fab

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Supramolecule #1: XG014 in complex with S trimer of SARS-CoV-2

SupramoleculeName: XG014 in complex with S trimer of SARS-CoV-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Fab fragment and S trimer generated by expression in 293 F cells
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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Supramolecule #2: S trimer of SARS-CoV-2

SupramoleculeName: S trimer of SARS-CoV-2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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Supramolecule #3: XG014 Fab

SupramoleculeName: XG014 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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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
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 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

Particle selectionNumber selected: 2977
CTF correctionSoftware - Name: RELION (ver. 3.0)
Startup modelType of model: EMDB MAP / Details: EMD-30326
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 342992
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model(PDB ID:

6vxx

,

6z3p

,

6pze

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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