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- EMDB-28756: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibo... -

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Entry
Database: EMDB / ID: EMD-28756
TitleStructure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3
Map data
Sample
  • Complex: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
    • Complex: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain
      • Protein or peptide: Antibody 1C3 Fab Heavy Chain
      • Protein or peptide: Antibody 1C3 Fab Light Chain
    • Complex: Spike glycoprotein
      • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN / glycoprotein / immune system / antibody / SARS-CoV-2 / COVID / VIRAL PROTEIN-Immune System complex / coronavirus
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 (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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsYu X / Zyla D / Hastie KM / Saphire EO
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
GHR Foundation United States
CitationJournal: Cell Rep / Year: 2023
Title: Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.
Authors: Kathryn M Hastie / Xiaoying Yu / Fernanda Ana-Sosa-Batiz / Dawid S Zyla / Stephanie S Harkins / Chitra Hariharan / Hal Wasserman / Michelle A Zandonatti / Robyn Miller / Erin Maule / Kenneth ...Authors: Kathryn M Hastie / Xiaoying Yu / Fernanda Ana-Sosa-Batiz / Dawid S Zyla / Stephanie S Harkins / Chitra Hariharan / Hal Wasserman / Michelle A Zandonatti / Robyn Miller / Erin Maule / Kenneth Kim / Kristen M Valentine / Sujan Shresta / Erica Ollmann Saphire /
Abstract: Therapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly ...Therapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly emergent strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), particularly those of the Omicron lineage. Here, we report the identification of a panel of vaccinee-derived antibodies that have broad-spectrum neutralization activity. Structural and biochemical characterization of the three broadest-spectrum antibodies reveal complementary footprints and differing requirements for avidity to overcome variant-associated mutations in their binding footprints. In the K18 mouse model of infection, these three antibodies exhibit protective efficacy against BA.1 and BA.2 infection. This study highlights the resilience and vulnerabilities of SARS-CoV-2 antibodies and provides road maps for further development of broad-spectrum therapeutics.
History
DepositionNov 2, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28756.png

Downloads & links

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Map

FileDownload / File: emd_28756.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.)
1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.34171963 - 1.1367804
Average (Standard dev.)-0.00012936915 (±0.019845225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28756_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28756_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibo...

EntireName: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
Components
  • Complex: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
    • Complex: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain
      • Protein or peptide: Antibody 1C3 Fab Heavy Chain
      • Protein or peptide: Antibody 1C3 Fab Light Chain
    • Complex: Spike glycoprotein
      • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibo...

SupramoleculeName: Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody 1C3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain

SupramoleculeName: Antibody 1C3 Fab Heavy Chain,Antibody 1C3 Fab Light Chain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Spike glycoprotein

SupramoleculeName: Spike glycoprotein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Antibody 1C3 Fab Heavy Chain

MacromoleculeName: Antibody 1C3 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.718235 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLLESGGG LVQPGRSLRL SCAASGFTFD DYAMHWVRQP PGKGLEWVSG SSWNSGSVVY ADSVKGRFTI SRDSAKNSLH LQMNSLRVE DTALYYCAKA VDPTRGSYSP DYGFDIWGQG TMVTVSS

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Macromolecule #2: Antibody 1C3 Fab Light Chain

MacromoleculeName: Antibody 1C3 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.554764 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DAIRMTQSPS SLSASVGDRV TITCRASQSI SSYLNWYQQK PGKAPNLLIY AASSLESGVP SRFSGSGSGT DFTLTISSLQ PEDFATYYC QQSYSTPLTF GGGTKVEIK

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Macromolecule #3: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 134.224359 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGVKVLFALI CIAVAEAQCV NLTTRTQLPP AYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH VISGTNGTKR FDNPVLPFN DGVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDHKNNK SWMESEFRVY S SANNCTFE ...String:
MGVKVLFALI CIAVAEAQCV NLTTRTQLPP AYTNSFTRGV YYPDKVFRSS VLHSTQDLFL PFFSNVTWFH VISGTNGTKR FDNPVLPFN DGVYFASIEK SNIIRGWIFG TTLDSKTQSL LIVNNATNVV IKVCEFQFCN DPFLDHKNNK SWMESEFRVY S SANNCTFE YVSQPFLMDL EGKQGNFKNL REFVFKNIDG YFKIYSKHTP IIVREPEDLP QGFSALEPLV DLPIGINITR FQ TLLALHR SYLTPGDSSS GWTAGAAAYY VGYLQPRTFL LKYNENGTIT DAVDCALDPL SETKCTLKSF TVEKGIYQTS NFR VQPTES IVRFPNITNL CPFDEVFNAT RFASVYAWNR KRISNCVADY SVLYNLAPFF TFKCYGVSPT KLNDLCFTNV YADS FVIRG DEVRQIAPGQ TGNIADYNYK LPDDFTGCVI AWNSNKLDSK VSGNYNYLYR LFRKSNLKPF ERDISTEIYQ AGNKP CNGV AGFNCYFPLR SYSFRPTYGV GHQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLKGTGVLT ESNKKF LPF QQFGRDIADT TDAVRDPQTL EILDITPCSF GGVSVITPGT NTSNQVAVLY QGVNCTEVPV AIHADQLTPT WRVYSTG SN VFQTRAGCLI GAEYVNNSYE CDIPIGAGIC ASYQTQTKSH GSASSVASQS IIAYTMSLGA ENSVAYSNNS IAIPTNFT I SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLKRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKYFGG FNFSQILPDP SKPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL ICAQKFKGLT VLPPLLTDEM IAQYTSALLA GTITSGWTF GAGPALQIPF PMQMAYRFNG IGVTQNVLYE NQKLIANQFN SAIGKIQDSL SSTPSALGKL QDVVNHNAQA L NTLVKQLS SKFGAISSVL NDIFSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KR VDFCGKG YHLMSFPQSA PHGVVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREGVFV SNGTHWFVTQ RNFYEPQIIT TDN TFVSGN CDVVIGIVNN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLID LQELG KYEQ

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 18 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / Details: TBS buffer pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
Details: home-made GO grids with continues graphene oxide layer
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.3.1) / Number images used: 49958
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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