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- EMDB-32516: SARS-CoV-2 spike protein in complex with three human neutralizing... -

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Basic information

Entry
Database: EMDB / ID: EMD-32516
TitleSARS-CoV-2 spike protein in complex with three human neutralizing antibodiesCoronavirus spike protein
Map dataSARS-CoV-2 spike protein in complex with three human neutralizing antibodiesCoronavirus spike protein
Sample
  • Complex: SARS-CoV-2 spike protein in complex with three human neutralizing antibodiesCoronavirus spike protein
    • Protein or peptide: Spike protein S1
    • Protein or peptide: XMA04 heavy chain variable domain
    • Protein or peptide: XMA01 heavy chain variable domain
    • Protein or peptide: IGL c4029_light_IGKV1-39_IGKJ2
    • Protein or peptide: IG c934_light_IGKV1-5_IGKJ1
    • Protein or peptide: XMA09 heavy chain variable domain
    • Protein or peptide: IG c1437_light_IGLV1-40_IGLJ1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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. ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IGL c4029_light_IGKV1-39_IGKJ2 / IG c934_light_IGKV1-5_IGKJ1 / IG c1437_light_IGLV1-40_IGLJ1 / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsZheng Q / Li S / Sun H / Zheng Z / Wang S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: Three SARS-CoV-2 antibodies provide broad and synergistic neutralization against variants of concern, including Omicron.
Authors: Siling Wang / Hui Sun / Yali Zhang / Lunzhi Yuan / Yizhen Wang / Tianying Zhang / Shaojuan Wang / Jinlei Zhang / Hai Yu / Hualong Xiong / Zimin Tang / Liqin Liu / Yang Huang / Xiuting Chen / ...Authors: Siling Wang / Hui Sun / Yali Zhang / Lunzhi Yuan / Yizhen Wang / Tianying Zhang / Shaojuan Wang / Jinlei Zhang / Hai Yu / Hualong Xiong / Zimin Tang / Liqin Liu / Yang Huang / Xiuting Chen / Tingting Li / Dong Ying / Chang Liu / Zihao Chen / Quan Yuan / Jun Zhang / Tong Cheng / Shaowei Li / Yi Guan / Qingbing Zheng / Zizheng Zheng / Ningshao Xia /
Abstract: The rapidly spreading Omicron variant is highly resistant to vaccines, convalescent sera, and neutralizing antibodies (nAbs), highlighting the urgent need for potent therapeutic nAbs. Here, a panel ...The rapidly spreading Omicron variant is highly resistant to vaccines, convalescent sera, and neutralizing antibodies (nAbs), highlighting the urgent need for potent therapeutic nAbs. Here, a panel of human nAbs from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent patients show diverse neutralization against Omicron, of which XMA01 and XMA04 maintain nanomolar affinities and excellent neutralization (half maximal inhibitory concentration [IC50]: ∼20 ng/mL). nAb XMA09 shows weak but unattenuated neutralization against all variants of concern (VOCs) as well as SARS-CoV. Structural analysis reveals that the above three antibodies could synergistically bind to the receptor-binding domains (RBDs) of both wild-type and Omicron spikes and defines the critical determinants for nAb-mediated broad neutralizations. Three nAbs confer synergistic neutralization against Omicron, resulting from the inter-antibody interaction between XMA04 and XMA01(or XMA09). Furthermore, the XMA01/XMA04 cocktail provides synergistic protection against Beta and Omicron variant infections in hamsters. In summary, our results provide insights for the rational design of antibody cocktail therapeutics or universal vaccines against Omicron.
History
DepositionJan 1, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32516.png

Downloads & links

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Map

FileDownload / File: emd_32516.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 spike protein in complex with three human neutralizing antibodies
Voxel sizeX=Y=Z: 0.778 Å
Density
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.67955315 - 1.0557504
Average (Standard dev.)-0.00027628723 (±0.015479835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 311.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 spike protein in complex with three human neutralizing...

EntireName: SARS-CoV-2 spike protein in complex with three human neutralizing antibodiesCoronavirus spike protein
Components
  • Complex: SARS-CoV-2 spike protein in complex with three human neutralizing antibodiesCoronavirus spike protein
    • Protein or peptide: Spike protein S1
    • Protein or peptide: XMA04 heavy chain variable domain
    • Protein or peptide: XMA01 heavy chain variable domain
    • Protein or peptide: IGL c4029_light_IGKV1-39_IGKJ2
    • Protein or peptide: IG c934_light_IGKV1-5_IGKJ1
    • Protein or peptide: XMA09 heavy chain variable domain
    • Protein or peptide: IG c1437_light_IGLV1-40_IGLJ1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 spike protein in complex with three human neutralizing...

SupramoleculeName: SARS-CoV-2 spike protein in complex with three human neutralizing antibodies
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: 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: 21.873496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGP

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Macromolecule #2: XMA04 heavy chain variable domain

MacromoleculeName: XMA04 heavy chain variable domain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.517036 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG VVQPGRSLRL SCAASGFTFR TYAMHWVRQA PGKGLEWVAV MWNDGSNKYY ADSVKGRFTI SRDNSKNTLY LEMNSLRAE DTAVYYCARE GVAAAGSSSD AFDIWGQGTM VTVSS

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Macromolecule #3: XMA01 heavy chain variable domain

MacromoleculeName: XMA01 heavy chain variable domain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.198615 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCSASGFTFS SYAMHWVRQA PGKGLEYVSS ISSNGGSTYY ADSVKGRFTI SRDNSKNTLY LQMSSLRVE DAAVYYCVKH YQQQLLWGGP DVWGQGTTVT VSS

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Macromolecule #4: IGL c4029_light_IGKV1-39_IGKJ2

MacromoleculeName: IGL c4029_light_IGKV1-39_IGKJ2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.616873 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS NFLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTLYSFG QGTKLEIK

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Macromolecule #5: IG c934_light_IGKV1-5_IGKJ1

MacromoleculeName: IG c934_light_IGKV1-5_IGKJ1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.781073 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPVS LSASVGDRVT ITCRASQSIS TWLAWYQQKP GKAPKLLIYE TSSLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QFNSYPWTFG QGTKVEIK

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Macromolecule #6: XMA09 heavy chain variable domain

MacromoleculeName: XMA09 heavy chain variable domain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.272664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFS SFAISWVRQA PGQGLEWMGG IIPIYGTANY AQKFQGRVTI TADESTSTAY MDLSSLRSE DTAVYYCARD GSSTYYPHNW FDPWGQGTLV TVSS

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Macromolecule #7: IG c1437_light_IGLV1-40_IGLJ1

MacromoleculeName: IG c1437_light_IGLV1-40_IGLJ1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.374391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG SGYDVHWYQQ LPGTAPKLLI YGNSNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDSSLSG VFGTGTKVTV L

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 721486

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