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- EMDB-68274: SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibo... -

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Basic information

Entry
Database: EMDB / ID: EMD-68274
TitleSARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibodies S2K146 and L4.65
Map data
Sample
  • Complex: SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibodies S2K146 and L4.65
    • Protein or peptide: Spike protein S1
    • Protein or peptide: The heavy chain of monoclonal antibody L4.65
    • Protein or peptide: The light chain of monoclonal antibody L4.65
    • Protein or peptide: The heavy chain of monoclonal antibody S2K146
    • Protein or peptide: The light chain of monoclonal antibody S2K146
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / BA.3.2.2 / RE.2.2 / RBD / monoclonal antibodiy / S2K146 / L4.65 / 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 / Lectin pathway of complement activation / host extracellular region / 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 / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane / identical protein binding / 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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 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: 3.19 Å
AuthorsLi LJ / Qu H / Wu QL / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Receptor Binding, Immune Escape, and Cross-Species Transmission of SARS-CoV-2 Serum-Defined Lineage 7, BA.3.2.2(RE.2.2)
Authors: Li LJ / Qu H / Wu QL / Gao GF
History
DepositionJan 11, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68274.png

Downloads & links

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Map

FileDownload / File: emd_68274.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.)
0.58 Å/pix.
x 400 pix.
= 232. Å		0.58 Å/pix.
x 400 pix.
= 232. Å		0.58 Å/pix.
x 400 pix.
= 232. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0017815571 - 2.3549058
Average (Standard dev.)0.0011351493 (±0.024779104)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 232.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68274_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_68274_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibo...

EntireName: SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibodies S2K146 and L4.65
Components
  • Complex: SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibodies S2K146 and L4.65
    • Protein or peptide: Spike protein S1
    • Protein or peptide: The heavy chain of monoclonal antibody L4.65
    • Protein or peptide: The light chain of monoclonal antibody L4.65
    • Protein or peptide: The heavy chain of monoclonal antibody S2K146
    • Protein or peptide: The light chain of monoclonal antibody S2K146
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibo...

SupramoleculeName: SARS-CoV-2 BA.3.2.2(RE.2.2) RBD in complex with monoclonal antibodies S2K146 and L4.65
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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 / Strain: BA.3.2.2 (RE.2.2)
Molecular weightTheoretical: 21.462082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CPFYEVFNAT RFPSVYAWNR TRISNCVADY SVLYNFAPFF TFKCYGVSPT KLNDLCFTNV YADSFVIKGN EVSQIAPGQT GNIADYNYK LPDDFTGCVI SWNSNRLDSK ADGNYNYWYR LFRKSKLKPF ERDISTEIYQ AGNNPCNGVK GFNCYFPLQS Y SFRPTYGV GYQPYRVVVL SFELLHAP

UniProtKB: Spike glycoprotein

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Macromolecule #2: The heavy chain of monoclonal antibody L4.65

MacromoleculeName: The heavy chain of monoclonal antibody L4.65 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.270899 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QITLKESGPT LVKPTQTLTL TCTFSGFSLS TSGVGVAWIR QPPGKALEWL ALIYWDNDKR SSPSLNNRLT ITKDTSKNQV VLTMTNMDP EDTATYYCAH FFSHYDSSNY YYGSWFDPWG QGTLVTVS

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Macromolecule #3: The light chain of monoclonal antibody L4.65

MacromoleculeName: The light chain of monoclonal antibody L4.65 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.796037 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSFD SRYLGWYQQK SGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQFGDSPFTF GQGTKLEIK

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Macromolecule #4: The heavy chain of monoclonal antibody S2K146

MacromoleculeName: The heavy chain of monoclonal antibody S2K146 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.207783 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGV VVQPGGSLRL SCAASGFTFH DHTMHWVRQA PGKGLEWVSL ITWNGGTIHY SDSVKGRFTI SRDNSKNSLY LQMNSLRTE DTALYYCAKD LGRGGWYLPS DAWGQGTLVT V

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Macromolecule #5: The light chain of monoclonal antibody S2K146

MacromoleculeName: The light chain of monoclonal antibody S2K146 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.637542 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PGQRVTISCS GSSANIGSNT VNWYQHLPGT APKLLIYSNN QRPSGVPSRF SGSKSGTSAS LAISGLQSSD EADYYCAAWD DSLKGVFGG GTKL

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: TFS FALCON 4i (4k x 4k) / #0 - Average electron dose: 50.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: TFS FALCON 4i (4k x 4k) / #1 - 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64297
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2
Image recording ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64297
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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