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- PDB-45id: Complex structure of THZ-939 Fab bound to SARS-CoV-2 WT RBD -

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Basic information

Entry
Database: PDB / ID: 45id
TitleComplex structure of THZ-939 Fab bound to SARS-CoV-2 WT RBD
Components
  • Spike protein S1
  • THZ-939 Fab Heavy chain
  • THZ-939 Fab Light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / RBD / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsWang, X. / Guo, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionAug 29, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: THZ-939 Fab Heavy chain
C: THZ-939 Fab Light chain
A: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)73,0913
Polymers73,0913
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-30 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.210, 108.210, 257.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody THZ-939 Fab Heavy chain


Mass: 24266.270 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 THZ-939 Fab Light chain


Mass: 23702.484 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 Spike protein S1


Mass: 25122.336 Da / Num. of mol.: 1 / Fragment: RBD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.04 Å3/Da / Density % sol: 79.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH7.5,10%(w/v)PEG8000;8%(v/v)Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.54→35.09 Å / Num. obs: 21976 / % possible obs: 99.44 % / Redundancy: 20 % / CC1/2: 0.998 / Net I/σ(I): 15.15
Reflection shellResolution: 3.54→3.67 Å / Num. unique obs: 2123 / CC1/2: 0.878

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.54→35.09 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1117 5.1 %
Rwork0.2372 --
obs0.2386 21903 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.54→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 0 0 4816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034948
X-RAY DIFFRACTIONf_angle_d0.5626735
X-RAY DIFFRACTIONf_dihedral_angle_d11.9961785
X-RAY DIFFRACTIONf_chiral_restr0.043750
X-RAY DIFFRACTIONf_plane_restr0.005871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.54-3.70.3471320.38292541X-RAY DIFFRACTION99
3.7-3.90.38741490.33282528X-RAY DIFFRACTION99
3.9-4.140.31061500.2982553X-RAY DIFFRACTION100
4.14-4.460.24061370.25072555X-RAY DIFFRACTION99
4.46-4.910.26071160.22082616X-RAY DIFFRACTION100
4.91-5.610.22441300.22372600X-RAY DIFFRACTION100
5.62-7.060.27171500.24722622X-RAY DIFFRACTION100
7.07-35.090.23281530.18682771X-RAY DIFFRACTION100

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