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- EMDB-32748: Structures of Omicron Spike complexes illuminate broad-spectrum n... -

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Basic information

Entry
Database: EMDB / ID: EMD-32748
TitleStructures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development
Map data
Sample
  • Complex: SARS-CoV-2 Omicron spike RBD complex with 510A5 Fab local refine
    • Complex: Omicron spike RBD
      • Protein or peptide: Spike protein S1
    • Complex: 510A5 Fab
      • Protein or peptide: 510A5 light chain
      • Protein or peptide: 510A5 heavy chain
KeywordsCOVID-19 / spike glycoprotein / virus / VIRAL PROTEIN / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGuo H / Gao Y
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentYDZX20213100001556 China
CitationJournal: Cell Rep / Year: 2022
Title: Structures of Omicron spike complexes and implications for neutralizing antibody development.
Authors: Hangtian Guo / Yan Gao / Tinghan Li / Tingting Li / Yuchi Lu / Le Zheng / Yue Liu / Tingting Yang / Feiyang Luo / Shuyi Song / Wei Wang / Xiuna Yang / Henry C Nguyen / Hongkai Zhang / Ailong ...Authors: Hangtian Guo / Yan Gao / Tinghan Li / Tingting Li / Yuchi Lu / Le Zheng / Yue Liu / Tingting Yang / Feiyang Luo / Shuyi Song / Wei Wang / Xiuna Yang / Henry C Nguyen / Hongkai Zhang / Ailong Huang / Aishun Jin / Haitao Yang / Zihe Rao / Xiaoyun Ji /
Abstract: The emergence of the SARS-CoV-2 Omicron variant is dominant in many countries worldwide. The high number of spike mutations is responsible for the broad immune evasion from existing vaccines and ...The emergence of the SARS-CoV-2 Omicron variant is dominant in many countries worldwide. The high number of spike mutations is responsible for the broad immune evasion from existing vaccines and antibody drugs. To understand this, we first present the cryo-electron microscopy structure of ACE2-bound SARS-CoV-2 Omicron spike. Comparison to previous spike antibody structures explains how Omicron escapes these therapeutics. Secondly, we report structures of Omicron, Delta, and wild-type spikes bound to a patient-derived Fab antibody fragment (510A5), which provides direct evidence where antibody binding is greatly attenuated by the Omicron mutations, freeing spike to bind ACE2. Together with biochemical binding and 510A5 neutralization assays, our work establishes principles of binding required for neutralization and clearly illustrates how the mutations lead to antibody evasion yet retain strong ACE2 interactions. Structural information on spike with both bound and unbound antibodies collectively elucidates potential strategies for generation of therapeutic antibodies.
History
DepositionJan 28, 2022-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32748.png

Downloads & links

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Map

FileDownload / File: emd_32748.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å		0.83 Å/pix.
x 512 pix.
= 425.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4056
Minimum - Maximum-0.9893383 - 2.8305554
Average (Standard dev.)-0.0017715977 (±0.021617109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.984 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 Omicron spike RBD complex with 510A5 Fab local refine

EntireName: SARS-CoV-2 Omicron spike RBD complex with 510A5 Fab local refine
Components
  • Complex: SARS-CoV-2 Omicron spike RBD complex with 510A5 Fab local refine
    • Complex: Omicron spike RBD
      • Protein or peptide: Spike protein S1
    • Complex: 510A5 Fab
      • Protein or peptide: 510A5 light chain
      • Protein or peptide: 510A5 heavy chain

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Supramolecule #1: SARS-CoV-2 Omicron spike RBD complex with 510A5 Fab local refine

SupramoleculeName: SARS-CoV-2 Omicron spike RBD complex with 510A5 Fab local refine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: local refine
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: Omicron spike RBD

SupramoleculeName: Omicron spike RBD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: SARS-CoV-2 Omicron variant spike protein ectodomain
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 510A5 Fab

SupramoleculeName: 510A5 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: Fab

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Macromolecule #1: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 1 / Details: Omicron / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 24.823148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN K PCNGVAGF ...String:
RVQPTESIVR FPNITNLCPF DEVFNATRFA SVYAWNRKRI SNCVADYSVL YNLAPFFTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKVSG NYNYLYRLFR KSNLKPFERD ISTEIYQAGN K PCNGVAGF NCYFPLRSYS FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN

UniProtKB: Spike glycoprotein

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Macromolecule #2: 510A5 light chain

MacromoleculeName: 510A5 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.680938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSIS SYLNWFQHKP GKAPKLLIYG ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYSTPPYTF GQGTKLEIK

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Macromolecule #3: 510A5 heavy chain

MacromoleculeName: 510A5 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.744181 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVQPGRSLRL SCAASGFTFD DYAMHWVRQA PGKGLEWVSG ISWNSDSIDY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTALYYCAKD RGYEILTPAS FDYWGQGTLV TVSSAS

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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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108540
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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