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- PDB-9xgx: Cryo-EM structure of SARS-CoV-2 receptor binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 9xgx
TitleCryo-EM structure of SARS-CoV-2 receptor binding domain in complex with SR-23 Fab (local refinement of RBD and Fv)
Components
  • Heavy chain of SR-23 Fab
  • Light chain of SR-23 Fab
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Viral 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 speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKim, U.J. / Wang, D.M. / Yoon, G.Y. / Cho, H.S.
Funding support Korea, Republic Of, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heavy chain of SR-23 Fab
B: Light chain of SR-23 Fab
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9284
Polymers46,7073
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Heavy chain of SR-23 Fab


Mass: 12577.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain of SR-23 Fab


Mass: 11810.103 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Spike protein S1


Mass: 22320.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sample sequence starts from 333
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1SARS-CoV-2 receptor binding domain in complex with SR-23 FabCOMPLEX#1-#30RECOMBINANT
2SARS-CoV-2 receptor binding domainCOMPLEX#31RECOMBINANT
3SR-23 FabCOMPLEX#1-#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.07 MDaYES
210.02 MDaYES
310.05 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Severe acute respiratory syndrome coronavirus 22697049
32Severe acute respiratory syndrome coronavirus 22697049
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Spodoptera frugiperda (fall armyworm)7108
43Homo sapiens (human)9606
Buffer solutionpH: 7.5 / Details: 20mM Tris-HCl, 150mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mMTris hydrochlorideC4H11NO31
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 105000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 67.6 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.2.1particle selectionblock picker and subsequent template picker were used to automatically select particle images.
2Topaz0.2.5particle selectionTopaz train model and Topaz picker were used to automatically select particle images.
8UCSF ChimeraXtech previewmodel fitting
12cryoSPARC4.2.1classificationheterogenous refinement was used to classify the particle images.
13cryoSPARC4.2.13D reconstructionlocal refinement using a mask covering RBD and Fab is used.
14PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2200000
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115041 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033326
ELECTRON MICROSCOPYf_angle_d0.4974521
ELECTRON MICROSCOPYf_dihedral_angle_d4.631483
ELECTRON MICROSCOPYf_chiral_restr0.042490
ELECTRON MICROSCOPYf_plane_restr0.005587

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