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- EMDB-66861: Cryo-EM structure of SARS-CoV-2 receptor binding domain in comple... -

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Entry
Database: EMDB / ID: EMD-66861
TitleCryo-EM structure of SARS-CoV-2 receptor binding domain in complex with SR-23 Fab (local refinement of RBD and Fv)
Map data
Sample
  • Complex: SARS-CoV-2 receptor binding domain in complex with SR-23 Fab
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Spike protein S1
    • Complex: SR-23 Fab
      • Protein or peptide: Heavy chain of SR-23 Fab
      • Protein or peptide: Light chain of SR-23 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsViral protein / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion / 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: 2.8 Å
AuthorsKim UJ / Wang DM / Yoon GY / Cho HS
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2024-00344154 Korea, Republic Of
National Research Foundation (NRF, Korea)2021M3A9I2080490 Korea, Republic Of
CitationJournal: J Med Virol / Year: 2026
Title: Broad Neutralizing Activity of Monoclonal Antibodies Against the Omicron Variants Isolated From Patients With Early Severe Acute Respiratory Syndrome Coronavirus-2.
Authors: Da Sol Kim / Uijin Kim / Hye-Min Woo / Hansaem Lee / Eun-Seong Jo / Min Jeong Noh / So-Young Lee / Byoung Kwon Park / Jeong-Sun Yang / Kyung-Chang Kim / Joo-Yeon Lee / Dong-Min Wang / Hyun- ...Authors: Da Sol Kim / Uijin Kim / Hye-Min Woo / Hansaem Lee / Eun-Seong Jo / Min Jeong Noh / So-Young Lee / Byoung Kwon Park / Jeong-Sun Yang / Kyung-Chang Kim / Joo-Yeon Lee / Dong-Min Wang / Hyun-Soo Cho / Hyun-Joo Kim /
Abstract: Since its emergence in 2019, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global pandemic driven by rapid mutation and high transmissibility. Current therapeutic ...Since its emergence in 2019, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused a global pandemic driven by rapid mutation and high transmissibility. Current therapeutic strategies may not effectively address the continuously evolving mutant strains, underscoring the need for treatments with broad neutralizing activity. Two monoclonal antibodies (mAbs): SR-23 and CS-42, isolated from convalescent patients infected with SARS-CoV-2 during the early phase of the 2020 pandemic, demonstrated significant neutralizing activities against a variety of variants. Specifically, SR-23 exhibited neutralizing activity against BA.5 and XBB1.5, whereas CS-42 showed efficacy against Delta, BA.1, and BA.2 variants. In addition, combining the two mAbs demonstrated improved neutralization activity. Cryo-electron microscopy (cryo-EM) structural analysis revealed that SR-23 and CS-42 bind to nonoverlapping epitopes on the SARS-CoV-2 spike protein. Furthermore, both antibodies exhibited strong therapeutic effects in K18-hACE2 mice infected with D614G, BA.2, and XBB.1.5. These findings provide insights into the development of antibody-based therapeutics targeting emerging Omicron variants and suggest that combined administration could broaden neutralizing activity.
History
DepositionOct 31, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66861.png

Downloads & links

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Map

FileDownload / File: emd_66861.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.4254607 - 2.2806716
Average (Standard dev.)-0.000015804702 (±0.038361765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66861_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_66861_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 receptor binding domain in complex with SR-23 Fab

EntireName: SARS-CoV-2 receptor binding domain in complex with SR-23 Fab
Components
  • Complex: SARS-CoV-2 receptor binding domain in complex with SR-23 Fab
    • Complex: SARS-CoV-2 receptor binding domain
      • Protein or peptide: Spike protein S1
    • Complex: SR-23 Fab
      • Protein or peptide: Heavy chain of SR-23 Fab
      • Protein or peptide: Light chain of SR-23 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 receptor binding domain in complex with SR-23 Fab

SupramoleculeName: SARS-CoV-2 receptor binding domain in complex with SR-23 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: SARS-CoV-2 receptor binding domain

SupramoleculeName: SARS-CoV-2 receptor binding domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: SR-23 Fab

SupramoleculeName: SR-23 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Heavy chain of SR-23 Fab

MacromoleculeName: Heavy chain of SR-23 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.577061 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LIQPGGSLRL SCAASGFTVS SNYMSWVRQA PGKGLEWVSV IFAGGSTFYA DSVKGRFTIS RDNSKNTLFL QLNSLRAED TAVYYCAREA ILRGTFDWGQ GTLVTVSS

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Macromolecule #2: Light chain of SR-23 Fab

MacromoleculeName: Light chain of SR-23 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.810103 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPVT LSVSPGERAT LSCRASQSVS SNLAWYQQKP GQAPRLLIYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYNNWPPGYT FGQGTKLEIK

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Macromolecule #3: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 3 / Details: Sample sequence starts from 333 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.320039 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGPKKS T

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / 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

Concentration0.05 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris hydrochloride

Details: 20mM Tris-HCl, 150mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #0 - Film thickness: 12 / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 67.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 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

Particle selectionNumber selected: 2200000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Software - details: local refinement using a mask covering RBD and Fab is used.
Number images used: 115041
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 100000 / Software - Name: cryoSPARC (ver. 4.2.1)
Software - details: heterogenous refinement was used to classify the particle images.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9xgx:
Cryo-EM structure of SARS-CoV-2 receptor binding domain in complex with SR-23 Fab (local refinement of RBD and Fv)

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