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- PDB-22pd: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937... -

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Basic information

Entry
Database: PDB / ID: 22pd
TitleCryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)
Components
  • SARS-CoV-2 BA.4 spike RBD
  • THZ937 fab heavy chain
  • THZ937 fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWang, X. / Guo, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Immunity / Year: 2026
Title: Twenty-year persistence of SARS-CoV-1 immune imprinting shapes antibody responses to SARS-CoV-2 infection.
Authors: Qi Zhang / Peng Chen / Fenglin Guo / Runhong Zhou / Ruihan Guo / Xiaofei Ge / Qianqian Yang / Xin Xie / Wei Xia / Junping Fan / Ziqing Yang / Yan Xu / Huiyu Huang / Jinqian Li / Han Wang / ...Authors: Qi Zhang / Peng Chen / Fenglin Guo / Runhong Zhou / Ruihan Guo / Xiaofei Ge / Qianqian Yang / Xin Xie / Wei Xia / Junping Fan / Ziqing Yang / Yan Xu / Huiyu Huang / Jinqian Li / Han Wang / Huiyu Liao / Xuanling Shi / Na Liu / Yuting Chen / Zhiwei Chen / Jianzhu Ma / Xinquan Wang / Tong Zhang / Linqi Zhang /
Abstract: Antibody imprinting is well recognized, yet its long-term dynamics and epitope specificity remain poorly understood. Here, we studied individuals sequentially infected with SARS-CoV-1 (SARS-1) and ...Antibody imprinting is well recognized, yet its long-term dynamics and epitope specificity remain poorly understood. Here, we studied individuals sequentially infected with SARS-CoV-1 (SARS-1) and SARS-CoV-2 (SARS-2) over two decades and found durable imprinting of antibody responses following SARS-2 BF.7 breakthrough infection. Approximately 60% of isolated monoclonal antibodies were SARS-1 imprinted and targeted conserved receptor-binding domain regions, whereas 37% overcame imprinting to recognize the SARS-2 receptor-binding motif overlapping the ACE2-binding site. Notably, some SARS-1-only antibodies retained germline-like features and neutralizing activity 20 years after infection. One exceptionally imprinted broadly neutralizing antibody, THZ937, protected hamsters against contact and airborne transmission of Omicron EG.5.1, demonstrating the functional relevance of durable imprinted antibodies. Together, these findings define the remarkable longevity and molecular basis of antibody imprinting and provide insights for pan-sarbecovirus vaccine design.
History
DepositionJan 19, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 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: THZ937 fab heavy chain
B: THZ937 fab light chain
C: SARS-CoV-2 BA.4 spike RBD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0374
Polymers48,8163
Non-polymers2211
Water00
1


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

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Components

#1: Antibody THZ937 fab heavy chain


Mass: 14117.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody THZ937 fab light chain


Mass: 12118.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein SARS-CoV-2 BA.4 spike RBD


Mass: 22579.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Production host: Homo sapiens (human)
#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 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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

ComponentName: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Severe acute respiratory syndrome coronavirus2901879
31Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 1500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.18.2_3874model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 537361 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0043471
ELECTRON MICROSCOPYf_angle_d0.7464723
ELECTRON MICROSCOPYf_dihedral_angle_d6.545491
ELECTRON MICROSCOPYf_chiral_restr0.048510
ELECTRON MICROSCOPYf_plane_restr0.005614

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