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- EMDB-15971: SARS-CoV-2 Delta-RBD complexed with Fabs BA.2-36, BA.2-23, EY6A a... -

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Basic information

Entry
Database: EMDB / ID: EMD-15971
TitleSARS-CoV-2 Delta-RBD complexed with Fabs BA.2-36, BA.2-23, EY6A and COVOX-45
Map dataCryoSPARC sharpened map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.
Sample
  • Complex: Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs
    • Complex: SARS-CoV2 delta variant receptor binding domain
      • Protein or peptide: Spike protein S1
    • Complex: Antibody chains
      • Protein or peptide: BA.2-23 heavy chainSARS-CoV-2 Omicron variant
      • Protein or peptide: BA.2-23 light chainSARS-CoV-2 Omicron variant
      • Protein or peptide: COVOX-45 heavy chain
      • Protein or peptide: COVOX-45 light chain
      • Protein or peptide: EY6A heavy chain
      • Protein or peptide: EY6A light chain
      • Protein or peptide: BA.2-36 heavy chainSARS-CoV-2 Omicron variant
      • Protein or peptide: BA.2-36 light chainSARS-CoV-2 Omicron variant
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
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 N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...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 N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDuyvesteyn HME / Ren J / Stuart DI
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell Rep / Year: 2023
Title: Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de ...Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de Silva / Megan Plowright / Thomas A H Newman / Hailey Hornsby / Alexander J Mentzer / Donal Skelly / Thomas G Ritter / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / / Cornelius Roemer / Thomas P Peacock / Neil G Paterson / Mark A Williams / David R Hall / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or ...In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
History
DepositionOct 17, 2022-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15971.png

Downloads & links

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Map

FileDownload / File: emd_15971.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC sharpened map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292.12 Å		0.73 Å/pix.
x 400 pix.
= 292.12 Å		0.73 Å/pix.
x 400 pix.
= 292.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7303 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.142
Minimum - Maximum-0.7574057 - 1.0798827
Average (Standard dev.)0.0005576215 (±0.019982925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.

Fileemd_15971_half_map_1.map
AnnotationHalf map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.

Fileemd_15971_half_map_2.map
AnnotationHalf map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs

EntireName: Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs
Components
  • Complex: Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs
    • Complex: SARS-CoV2 delta variant receptor binding domain
      • Protein or peptide: Spike protein S1
    • Complex: Antibody chains
      • Protein or peptide: BA.2-23 heavy chainSARS-CoV-2 Omicron variant
      • Protein or peptide: BA.2-23 light chainSARS-CoV-2 Omicron variant
      • Protein or peptide: COVOX-45 heavy chain
      • Protein or peptide: COVOX-45 light chain
      • Protein or peptide: EY6A heavy chain
      • Protein or peptide: EY6A light chain
      • Protein or peptide: BA.2-36 heavy chainSARS-CoV-2 Omicron variant
      • Protein or peptide: BA.2-36 light chainSARS-CoV-2 Omicron variant

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Supramolecule #1: Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs

SupramoleculeName: Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all

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Supramolecule #2: SARS-CoV2 delta variant receptor binding domain

SupramoleculeName: SARS-CoV2 delta variant receptor binding domain / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Antibody chains

SupramoleculeName: Antibody chains / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.935734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHTNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYRYRL FRKSNLKPFE RDISTEIYQA GSKPCNGVEG F NCYFPLQS ...String:
HHHHHHTNLC PFGEVFNATR FASVYAWNRK RISNCVADYS VLYNSASFST FKCYGVSPTK LNDLCFTNVY ADSFVIRGDE VRQIAPGQT GKIADYNYKL PDDFTGCVIA WNSNNLDSKV GGNYNYRYRL FRKSNLKPFE RDISTEIYQA GSKPCNGVEG F NCYFPLQS YGFQPTNGVG YQPYRVVVLS FELLHAPATV CGKK

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Macromolecule #2: BA.2-23 heavy chain

MacromoleculeName: BA.2-23 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.781458 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG LVQPGGSLRL SCEVSGFTVT VNYMTWVRQA PGQGLEWVAM IYSGGSTFYA DSVKGRFTIS RHNSKNTLFL QMNSLRPED TAVYYCARPI VGGIAGMDVW GLGTTVTVSS

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Macromolecule #3: BA.2-23 light chain

MacromoleculeName: BA.2-23 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.804117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIRMTQSPSS LSASVGDRIT ITCQASQDIN KYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTINSLQP EDIATYYCQ QHDNIPITFG QGTRLEIK

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Macromolecule #4: COVOX-45 heavy chain

MacromoleculeName: COVOX-45 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.187152 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGRSLRL SCAASGFTFS TYAMHWVRQA PGKGLEWVAV LSYDGSNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKG GSYAYYYYMD VWGKGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS TYAMHWVRQA PGKGLEWVAV LSYDGSNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKG GSYAYYYYMD VWGKGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDK

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Macromolecule #5: COVOX-45 light chain

MacromoleculeName: COVOX-45 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.599754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPSS LSASVGDRVT ITCQASQDIS NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGGGSGTD FTFTITSLQP EDIATYYCQ QYDNLPLTFG GGTKVDIK

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Macromolecule #6: EY6A heavy chain

MacromoleculeName: EY6A heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.506048 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG VVQPGRSLRL SCAASAFTFS SYDMHWVRQA PGKGLEWVAV ISYDGSNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCAKD GGKLWVYYFD YWGQGTLVTV SS

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Macromolecule #7: EY6A light chain

MacromoleculeName: EY6A light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.555833 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTLALTF GGGTKVEIK

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Macromolecule #8: BA.2-36 heavy chain

MacromoleculeName: BA.2-36 heavy chain / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.00936 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGPG RVKPSQTLSL TCTVSGDSIN SGINYWNWIR QPAGKELEWI GRIFTSGTTH YNPSLKSRVT ISVDRSKNEF SLTLNSVTA ADTAVYFCGR GGTDDYVDYW GQGTLVTVSS

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Macromolecule #9: BA.2-36 light chain

MacromoleculeName: BA.2-36 light chain / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.679038 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIQMTQSPST LSASVGDRVT ITCRASQDIN SWLAWYQQKP GKAPKLLIYD ASSLHSGVPT RFSGSGSGTE FTLTISSLQP DDFASYYCQ QYKSYRTFGR GTKVEIK

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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: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7nx9


Details: RBD, BA.2-23 and EY6A from PDB 7NX9, COVOX45 from pdb 7BEL, RBD and BA.2-36 Fab from 8BBO.
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 167492

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