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- EMDB-68583: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937... -

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Basic information

Entry
Database: EMDB / ID: EMD-68583
TitleCryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)
Map data
Sample
  • Complex: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)
    • Protein or peptide: THZ937 fab heavy chain
    • Protein or peptide: THZ937 fab light chain
    • Protein or peptide: SARS-CoV-2 BA.4 spike RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesSevere acute respiratory syndrome coronavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsWang X / Guo F
Funding support China, 1 items
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, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68583.png

Downloads & links

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Map

FileDownload / File: emd_68583.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å		1.08 Å/pix.
x 192 pix.
= 207.84 Å

Surface

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Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.145
Minimum - Maximum-0.6572577 - 1.2221785
Average (Standard dev.)0.0053154114 (±0.033819538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 207.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68583_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68583_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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

EntireName: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)
Components
  • Complex: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)
    • Protein or peptide: THZ937 fab heavy chain
    • Protein or peptide: THZ937 fab light chain
    • Protein or peptide: SARS-CoV-2 BA.4 spike RBD
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937...

SupramoleculeName: Cryo EM structure of SARS-COV-2 (BA.4) RBD in complex with THZ937 Fab (local refine)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus

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Macromolecule #1: THZ937 fab heavy chain

MacromoleculeName: THZ937 fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.11755 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LIQPGGSLRL SCAASGFSVS TNYMSWVRQA PGKGLEWVSV IYGGDTTYYA DSVRGRFTIS RDNSKNTLYL EMNSLRTDD TAVYYCARDE GRYFDIWTGH VGPNCFDYWG QGTLVTVSS

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Macromolecule #2: THZ937 fab light chain

MacromoleculeName: THZ937 fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.118496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPSS LSASVGDRVT ITCRASQSIS TYLNWYQQKP GKAPKLLIYG ASNLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSYITLVTFG QGTRLEIKRT VAA

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Macromolecule #3: SARS-CoV-2 BA.4 spike RBD

MacromoleculeName: SARS-CoV-2 BA.4 spike RBD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 22.5795 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNFAP FFAFKCYGVS PTKLNDLCFT NVYADSFVIR GNEVSQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKVGGNYNYR YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGVNCYFPL Q SYGFRPTY ...String:
NLCPFDEVFN ATRFASVYAW NRKRISNCVA DYSVLYNFAP FFAFKCYGVS PTKLNDLCFT NVYADSFVIR GNEVSQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKVGGNYNYR YRLFRKSNLK PFERDISTEI YQAGNKPCNG VAGVNCYFPL Q SYGFRPTY GVGHQPYRVV VLSFELLHAP ATVCGPKKST NL

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 1.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 537361
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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