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- EMDB-16375: SARS-CoV2 Omicron BA.1 RBD in complex with CAB-A17 antibody -

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Basic information

Entry
Database: EMDB / ID: EMD-16375
TitleSARS-CoV2 Omicron BA.1 RBD in complex with CAB-A17 antibody
Map data
Sample
  • Complex: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
    • Complex: SARS-CoV-2 Omicron RBD
      • Protein or peptide: Spike protein S2'
    • Complex: CAB-A17 Antibody (Fab)
      • Protein or peptide: CAB-A17 antibody (variable)
      • Protein or peptide: CAB-A17 antibody (variable)
KeywordsAntibody / Spike / Complex / VIRAL PROTEIN
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 speciesSevere acute respiratory syndrome coronavirus 2 / Enterobacteria phage T4 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsDas H / Hallberg BM
Funding support1 items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Cell Rep Med / Year: 2024
Title: Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies.
Authors: Daniel J Sheward / Pradeepa Pushparaj / Hrishikesh Das / Allison J Greaney / Changil Kim / Sungyong Kim / Leo Hanke / Erik Hyllner / Robert Dyrdak / Jimin Lee / Xaquin Castro Dopico / Pia ...Authors: Daniel J Sheward / Pradeepa Pushparaj / Hrishikesh Das / Allison J Greaney / Changil Kim / Sungyong Kim / Leo Hanke / Erik Hyllner / Robert Dyrdak / Jimin Lee / Xaquin Castro Dopico / Pia Dosenovic / Thomas P Peacock / Gerald M McInerney / Jan Albert / Martin Corcoran / Jesse D Bloom / Ben Murrell / Gunilla B Karlsson Hedestam / B Martin Hällberg /
Abstract: Descendants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant now account for almost all SARS-CoV-2 infections. The Omicron variant and its sublineages have spike ...Descendants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant now account for almost all SARS-CoV-2 infections. The Omicron variant and its sublineages have spike glycoproteins that are highly diverged from the pandemic founder and first-generation vaccine strain, resulting in significant evasion from monoclonal antibody therapeutics and vaccines. Understanding how commonly elicited antibodies can broaden to cross-neutralize escape variants is crucial. We isolate IGHV3-53, using "public" monoclonal antibodies (mAbs) from an individual 7 months post infection with the ancestral virus and identify antibodies that exhibit potent and broad cross-neutralization, extending to the BA.1, BA.2, and BA.4/BA.5 sublineages of Omicron. Deep mutational scanning reveals these mAbs' high resistance to viral escape. Structural analysis via cryoelectron microscopy of a representative broadly neutralizing antibody, CAB-A17, in complex with the Omicron BA.1 spike highlights the structural underpinnings of this broad neutralization. By reintroducing somatic hypermutations into a germline-reverted CAB-A17, we delineate the role of affinity maturation in the development of cross-neutralization by a public class of antibodies.
#1: Journal: Biochem Biophys Res Commun / Year: 1975
Title: Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution.
Authors: Bose KS / Sarma RH
History
DepositionDec 19, 2022-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16375.png

Downloads & links

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Map

FileDownload / File: emd_16375.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 600 pix.
= 606. Å		1.01 Å/pix.
x 600 pix.
= 606. Å		1.01 Å/pix.
x 600 pix.
= 606. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-2.441012 - 6.2398143
Average (Standard dev.)-0.0019176095 (±0.03475844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 606.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16375_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_16375_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody

EntireName: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
Components
  • Complex: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
    • Complex: SARS-CoV-2 Omicron RBD
      • Protein or peptide: Spike protein S2'
    • Complex: CAB-A17 Antibody (Fab)
      • Protein or peptide: CAB-A17 antibody (variable)
      • Protein or peptide: CAB-A17 antibody (variable)

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Supramolecule #1: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody

SupramoleculeName: SARS-CoV2 Omicron BA.1 Spike in complex with CAB-A17 antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 95.7 KDa

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Supramolecule #2: SARS-CoV-2 Omicron RBD

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

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Supramolecule #3: CAB-A17 Antibody (Fab)

SupramoleculeName: CAB-A17 Antibody (Fab) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Enterobacteria phage T4 (virus)

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Macromolecule #1: Spike protein S2'

MacromoleculeName: Spike protein S2' / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.942738 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKVSGNYNYL YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGFNCYFPL R SYSFRPTY ...String:
NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKVSGNYNYL YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGFNCYFPL R SYSFRPTY GVGHQPYRVV VLSFELLHAP ATVCG

UniProtKB: Spike glycoprotein

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Macromolecule #2: CAB-A17 antibody (variable)

MacromoleculeName: CAB-A17 antibody (variable) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.395632 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAS LSCRASQSLS TYLAWYQQKP GQAPRLLIFG ASSRASGIPD RFSGGGSGTD FTLTISRLEP EDFAVYYCQ QYGSSPRTFG QGTKVEI

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Macromolecule #3: CAB-A17 antibody (variable)

MacromoleculeName: CAB-A17 antibody (variable) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.839197 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DVHLVESGGG LIQPGGSLRL SCAASEFIVS ANYMSWVRQA PGEGLQWVSV IYPGGSTFYA ESVKGRFTIS RDNSRNTLYL QMNSLRAED TGVYYCARDY GDFYFDYWGQ GTLVTVS

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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

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 25652 / Average exposure time: 1.5 sec. / Average electron dose: 54.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 165000
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: PDB ENTRY
PDB model - PDB ID:

7a29


Details: 7A29 and 7K8M
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 199751
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7ksg


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 142
Output model

PDB-8c0y:
SARS-CoV2 Omicron BA.1 RBD in complex with CAB-A17 antibody

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