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- EMDB-30863: Cryo-electron microscopy density map of the the RBD in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-30863
TitleCryo-electron microscopy density map of the the RBD in complex with MA1ScFv, MA2Fab
Map data
Sample
  • Complex: SARS-CoV-2 RBD in complex with MA1ScFv and MA2Fab
    • Complex: SARS-CoV-2 RBD
    • Complex: MA1ScFv and MA2Fab
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsJia LN / Liu YP / Tian LF / Xiong C / Xu X / Qu H / Xiong WX / Zhou D / Wang F / Liu Z ...Jia LN / Liu YP / Tian LF / Xiong C / Xu X / Qu H / Xiong WX / Zhou D / Wang F / Liu Z / Yan XX / Xu WQ / Tang L
CitationJournal: MedComm (2020) / Year: 2021
Title: Potent neutralizing RBD-specific antibody cocktail against SARS-CoV-2 and its mutant.
Authors: Lina Jia / Yan-Ping Liu / Li-Fei Tian / Chao Xiong / Xin Xu / Honge Qu / Weixi Xiong / Dong Zhou / Feng Wang / Zheng Liu / Xiao-Xue Yan / Wenqing Xu / Lin Tang /
Abstract: The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants has posed a serious global public health emergency. Therapeutic interventions or vaccines ...The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants has posed a serious global public health emergency. Therapeutic interventions or vaccines are urgently needed to treat and prevent the further dissemination of this contagious virus. This study described the identification of neutralizing receptor-binding domain (RBD)-specific antibodies from mice through vaccination with a recombinant SARS-CoV-2 RBD. RBD-targeted monoclonal antibodies (mAbs) with distinct function and epitope recognition were selected to understand SARS-CoV-2 neutralization. High-affinity RBD-specific antibodies exhibited high potency in neutralizing both live and pseudotype SARS-CoV-2 viruses and the SARS-CoV-2 pseudovirus particle containing the spike protein S-RBD mutant (SARS-CoV-2(V367F)). These results demonstrated that these antibodies recognize four distinct groups (I-IV) of epitopes on the RBD and that mAbs targeting group I epitope can be used in combination with mAbs recognizing groups II and/or IV epitope to make mAb cocktails against SARS-CoV-2 and its mutants. Moreover, structural characterization reveals that groups I, III, and IV epitopes are closely located to an RBD hotspot. The identification of RBD-specific antibodies and cocktails may provide an effective therapeutic and prophylactic intervention against SARS-CoV-2 and its isolates.
History
DepositionJan 7, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateJul 20, 2022-
Current statusJul 20, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0156
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30863.png

Downloads & links

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Map

FileDownload / File: emd_30863.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 160 pix.
= 163.2 Å		1.02 Å/pix.
x 160 pix.
= 163.2 Å		1.02 Å/pix.
x 160 pix.
= 163.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0156 / Movie #1: 0.0156
Minimum - Maximum-0.112019174 - 0.18901968
Average (Standard dev.)-8.675444e-06 (±0.005108161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 163.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z163.200163.200163.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1120.189-0.000

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 RBD in complex with MA1ScFv and MA2Fab

EntireName: SARS-CoV-2 RBD in complex with MA1ScFv and MA2Fab
Components
  • Complex: SARS-CoV-2 RBD in complex with MA1ScFv and MA2Fab
    • Complex: SARS-CoV-2 RBD
    • Complex: MA1ScFv and MA2Fab

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Supramolecule #1: SARS-CoV-2 RBD in complex with MA1ScFv and MA2Fab

SupramoleculeName: SARS-CoV-2 RBD in complex with MA1ScFv and MA2Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 103 KDa

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Supramolecule #2: SARS-CoV-2 RBD

SupramoleculeName: SARS-CoV-2 RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Insecta (insects)

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Supramolecule #3: MA1ScFv and MA2Fab

SupramoleculeName: MA1ScFv and MA2Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Details: blot for 5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3105 / Average electron dose: 58.44 e/Å2 / Details: Preliminary grid screening was performed manually
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 122418
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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