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- EMDB-34808: SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A -

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Basic information

Entry
Database: EMDB / ID: EMD-34808
TitleSARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A
Map data
Sample
  • Complex: Complex of Delta Spike and IY-2A with two Fabs bound to one Spike in 3-RBD-up conformation
    • Complex: SARS-CoV-2 Delta Spike protein
      • Protein or peptide: Spike glycoprotein
    • Complex: IY-2A
      • Protein or peptide: IY-2A Fab heavy chain
      • Protein or peptide: IY-2A Fab light chain
KeywordsSpike / Omicron variant / BA.1 / RBD / monoclonal antibody / Fab / IY-2A / class 4 / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / viral translation / host extracellular space / 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 / viral translation / host extracellular space / 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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsChen X / Mohapatra A / Wu Y-M
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Authors: Kuan-Ying A Huang / Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Susan K Vester / Rory A Hills / Mark Howarth / Jennifer R Keeffe ...Authors: Kuan-Ying A Huang / Xiaorui Chen / Arpita Mohapatra / Hong Thuy Vy Nguyen / Lisa Schimanski / Tiong Kit Tan / Pramila Rijal / Susan K Vester / Rory A Hills / Mark Howarth / Jennifer R Keeffe / Alexander A Cohen / Leesa M Kakutani / Yi-Min Wu / Md Shahed-Al-Mahmud / Yu-Chi Chou / Pamela J Bjorkman / Alain R Townsend / Che Ma /
Abstract: Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural ...Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.
History
DepositionNov 17, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34808.png

Downloads & links

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Map

FileDownload / File: emd_34808.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 324 pix.
= 343.44 Å		1.06 Å/pix.
x 324 pix.
= 343.44 Å		1.06 Å/pix.
x 324 pix.
= 343.44 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0037
Minimum - Maximum-0.02604841 - 0.04447294
Average (Standard dev.)0.000013066992 (±0.0014210356)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 343.43997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34808_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_34808_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Delta Spike and IY-2A with two Fabs bound to one Spike...

EntireName: Complex of Delta Spike and IY-2A with two Fabs bound to one Spike in 3-RBD-up conformation
Components
  • Complex: Complex of Delta Spike and IY-2A with two Fabs bound to one Spike in 3-RBD-up conformation
    • Complex: SARS-CoV-2 Delta Spike protein
      • Protein or peptide: Spike glycoprotein
    • Complex: IY-2A
      • Protein or peptide: IY-2A Fab heavy chain
      • Protein or peptide: IY-2A Fab light chain

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Supramolecule #1: Complex of Delta Spike and IY-2A with two Fabs bound to one Spike...

SupramoleculeName: Complex of Delta Spike and IY-2A with two Fabs bound to one Spike in 3-RBD-up conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 550 KDa

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Supramolecule #2: SARS-CoV-2 Delta Spike protein

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

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Supramolecule #3: IY-2A

SupramoleculeName: IY-2A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 140.204906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVKLLVLLC TFTATYAGTQ CVNLTTRTQL PPAYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHVISGTNGT KRFDNPVLP FNDGVYFASI EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLDHKN NKSWMESEFR V YSSANNCT ...String:
MKVKLLVLLC TFTATYAGTQ CVNLTTRTQL PPAYTNSFTR GVYYPDKVFR SSVLHSTQDL FLPFFSNVTW FHVISGTNGT KRFDNPVLP FNDGVYFASI EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLDHKN NKSWMESEFR V YSSANNCT FEYVSQPFLM DLEGKQGNFK NLREFVFKNI DGYFKIYSKH TPIIVREPED LPQGFSALEP LVDLPIGINI TR FQTLLAL HRSYLTPGDS SSGWTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSN FRVQPT ESIVRFPNIT NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNLAP FFTFKCYGVS PTKLNDLCFT NVYA DSFVI RGDEVRQIAP GQTGNIADYN YKLPDDFTGC VIAWNSNKLD SKVSGNYNYL YRLFRKSNLK PFERDISTEI YQAGN KPCN GVAGFNCYFP LRSYSFRPTY GVGHQPYRVV VLSFELLHAP ATVCGPKKST NLVKNKCVNF NFNGLKGTGV LTESNK KFL PFQQFGRDIA DTTDAVRDPQ TLEILDITPC SFGGVSVITP GTNTSNQVAV LYQGVNCTEV PVAIHADQLT PTWRVYS TG SNVFQTRAGC LIGAEYVNNS YECDIPIGAG ICASYQTQTK SHGSASSVAS QSIIAYTMSL GAENSVAYSN NSIAIPTN F TISVTTEILP VSMTKTSVDC TMYICGDSTE CSNLLLQYGS FCTQLKRALT GIAVEQDKNT QEVFAQVKQI YKTPPIKYF GGFNFSQILP DPSKPSKRSF IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFKG LTVLPPLLTD EMIAQYTSAL LAGTITSGW TFGAGAALQI PFAMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLSSTASALG KLQDVVNHNA Q ALNTLVKQ LSSKFGAISS VLNDIFSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QS KRVDFCG KGYHLMSFPQ SAPHGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRNFYEPQI ITT DNTFVS GNCDVVIGIV NNTVYDPLQP ELDSFKEELD KYFKNHTSPD VDLGDISGIN ASVVNIQKEI DRLNEVAKNL NESL IDLQE LGKYEQYIKD IRSLVPRGSP GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG HHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: IY-2A Fab heavy chain

MacromoleculeName: IY-2A Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.576566 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVEWGAG LLKPSETLSL TCAVYGGSFS GYYWSWIRQP PGKGLEWIGL INHSGSTNYN PSLKSRVTIS LDTSKNQFSL KLTSVTAAD TAVYYCARGL GIFGVVTLSD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVEWGAG LLKPSETLSL TCAVYGGSFS GYYWSWIRQP PGKGLEWIGL INHSGSTNYN PSLKSRVTIS LDTSKNQFSL KLTSVTAAD TAVYYCARGL GIFGVVTLSD VWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSC

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Macromolecule #3: IY-2A Fab light chain

MacromoleculeName: IY-2A Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.078279 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: NFMLTQPHSV SESPGKTVTI SCTGSSGSIA SNYVQWYQQR PGSAPTTVIY EDNQRPSGVP DRFSGSIDSS SNSASLTISG LRTEDEADY YCQSYDSGIW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
NFMLTQPHSV SESPGKTVTI SCTGSSGSIA SNYVQWYQQR PGSAPTTVIY EDNQRPSGVP DRFSGSIDSS SNSASLTISG LRTEDEADY YCQSYDSGIW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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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

Concentration0.8 mg/mL
BufferpH: 7.5 / Details: 20mM Tris pH 7.5 150mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 258 K / Instrument: FEI VITROBOT MARK IV
Detailsfreshly mixed (3 min at room temperature) for complex formation

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4685 / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1405490
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xo5

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 67276
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 3 / Avg.num./class: 25000 / Software - Name: RELION (ver. 3.0)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8hhz:
SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A

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