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- EMDB-31639: SARS-CoV-2 Spike trimer in complex with XG014 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-31639
TitleSARS-CoV-2 Spike trimer in complex with XG014 Fab
Map data
SampleXG014 in complex with S trimer of SARS-CoV-2:
S trimer of SARS-CoV-2 / XG014 / Spike glycoproteinSpike protein / The light chain of XG014 Fab / The heavy chain of XG014 / ligand
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / viral translation / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / viral translation / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / : / viral entry into host cell / viral envelope / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
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 / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / : / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / : / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang K / Wang X / Pan L
Funding support China, 1 items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Protein Cell / Year: 2021
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 7, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7v2a
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7v2a
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31639.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
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.03441124 - 0.07105861
Average (Standard dev.)6.661768e-06 (±0.0017931656)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0340.0710.000

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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
Details: Fab fragment and S trimer generated by expression in 293 F cells
Number of Components: 7

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Component #1: protein, XG014 in complex with S trimer of SARS-CoV-2

ProteinName: XG014 in complex with S trimer of SARS-CoV-2
Details: Fab fragment and S trimer generated by expression in 293 F cells
Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #2: protein, S trimer of SARS-CoV-2

ProteinName: S trimer of SARS-CoV-2 / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Component #3: protein, XG014

ProteinName: XG014 / Recombinant expression: No

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Component #4: protein, Spike glycoprotein

ProteinName: Spike glycoproteinSpike protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 133.75325 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, The light chain of XG014 Fab

ProteinName: The light chain of XG014 Fab / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 22.632064 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, The heavy chain of XG014

ProteinName: The heavy chain of XG014 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 25.897936 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 24 / 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 solutionSpecimen conc.: 0.8 mg/mL / pH: 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
LensCs: 2.7 mm / Imaging Mode: DARK FIELD / Defocus: 1200.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 414922
3D reconstructionResolution: 3.4 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 6VXX, 6Z3P, 6PZE
Output model

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