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- EMDB-47426: CryoEM structure of a broadly neutralizing anti-SARS-CoV-2 antibody 52 -

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Basic information

Entry
Database: EMDB / ID: EMD-47426
TitleCryoEM structure of a broadly neutralizing anti-SARS-CoV-2 antibody 52
Map data
Sample
  • Complex: 52 Fab complex with RBD on XBB.1.5 spike
    • Protein or peptide: 52 Fab Heavy chain
    • Protein or peptide: 52 Fab light chain
    • Protein or peptide: SARS XBB.1.5 Spike
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Antibody / RBD / Immune system / Viral protein-immune system complex
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJaiswal D / Bajic G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI168178 United States
CitationJournal: Sci Immunol / Year: 2025
Title: Germinal center-mediated broadening of B cell responses to SARS-CoV-2 booster immunization.
Authors: Sameer Kumar Malladi / Deepika Jaiswal / Baoling Ying / Wafaa B Alsoussi / Tamarand L Darling / Bernadeta Dadonaite / Alesandro Civljak / Stephen C Horvath / Julian Q Zhou / Wooseob Kim / ...Authors: Sameer Kumar Malladi / Deepika Jaiswal / Baoling Ying / Wafaa B Alsoussi / Tamarand L Darling / Bernadeta Dadonaite / Alesandro Civljak / Stephen C Horvath / Julian Q Zhou / Wooseob Kim / Jackson S Turner / Aaron J Schmitz / Fangjie Han / Suzanne M Scheaffer / Christopher W Farnsworth / Raffael Nachbagauer / Biliana Nestorova / Spyros Chalkias / Michael K Klebert / Darin K Edwards / Robert Paris / Benjamin S Strnad / William D Middleton / Jane A O'Halloran / Rachel M Presti / Jesse D Bloom / Adrianus C M Boon / Michael S Diamond / Goran Bajic / Ali H Ellebedy /
Abstract: Germinal centers (GCs) are key sites for antibody diversification and affinity maturation. SARS-CoV-2 messenger RNA (mRNA) vaccines elicit robust GC B cell responses in humans, but how these ...Germinal centers (GCs) are key sites for antibody diversification and affinity maturation. SARS-CoV-2 messenger RNA (mRNA) vaccines elicit robust GC B cell responses in humans, but how these responses influence the breadth of immunity against viral variants remains unclear. We analyzed GC B cell responses in nine healthy adults after mRNA booster immunization. We show that 77.8% of the B cell clones in the GC expressed representative monoclonal antibodies (mAbs) recognizing the spike protein, with 37.8% of these targeting the receptor binding domain (RBD). One RBD-targeting mAb, mAb-52, neutralized all tested SARS-CoV-2 strains, including the recent XEC variant. mAb-52 used the public clonotype, protected hamsters challenged against the EG.5.1 variant, and targeted the class I/II RBD epitope, closely mimicking the binding footprint of ACE2. Its broad reactivity was driven by extensive somatic hypermutation, underscoring the critical role of GC reactions in shaping cross-variant B cell immunity after SARS-CoV-2 booster vaccination.
History
DepositionOct 21, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47426.png

Downloads & links

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Map

FileDownload / File: emd_47426.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 422.4 Å		0.83 Å/pix.
x 512 pix.
= 422.4 Å		0.83 Å/pix.
x 512 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.0017482857 - 2.3104095
Average (Standard dev.)0.00025889283 (±0.009328299)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47426_additional_1.map
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Half map: #1

Fileemd_47426_half_map_1.map
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Histogram (log scale)

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Half map: #2

Fileemd_47426_half_map_2.map
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Sample components

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Entire : 52 Fab complex with RBD on XBB.1.5 spike

EntireName: 52 Fab complex with RBD on XBB.1.5 spike
Components
  • Complex: 52 Fab complex with RBD on XBB.1.5 spike
    • Protein or peptide: 52 Fab Heavy chain
    • Protein or peptide: 52 Fab light chain
    • Protein or peptide: SARS XBB.1.5 Spike
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 52 Fab complex with RBD on XBB.1.5 spike

SupramoleculeName: 52 Fab complex with RBD on XBB.1.5 spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Macromolecule #1: 52 Fab Heavy chain

MacromoleculeName: 52 Fab Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.572168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVQSGGDL APPGGSLRLS CEASGIIVSS NYMTWVRQAP GKGLEWVSLI FAGGSTFYAD SVKGRFTVSR DNSKNTLYLQ MSSLKPEDT AVYFCARDLR EMGGLDFWGQ GALVTVSS

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Macromolecule #2: 52 Fab light chain

MacromoleculeName: 52 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.220589 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQMTQSPSSV SASIGDTVTI TCRASQGIPS WVAWYQQKPG KAPKLLIYGA SNLQRGVPSR FSGSGSGTDF TLTISSLQPE DLAVYYCHQ SDSLPGIFGG GTKVEIK

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Macromolecule #3: SARS XBB.1.5 Spike

MacromoleculeName: SARS XBB.1.5 Spike / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 22.666639 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VRFPNITNLC PFHEVFNATT FASVYAWNRK RISNCVADYS VIYNFAPFFA FKCYGVSPTK LNDLCFTNVY ADSFVIRGNE VSQIAPGQT GNIADYNYKL PDDFTGCVIA WNSNKLDSKP SGNYNYLYRF LRKSKLKPFE RDISTEIYQV GNKPCNGVAG P NCYSPLQS ...String:
VRFPNITNLC PFHEVFNATT FASVYAWNRK RISNCVADYS VIYNFAPFFA FKCYGVSPTK LNDLCFTNVY ADSFVIRGNE VSQIAPGQT GNIADYNYKL PDDFTGCVIA WNSNKLDSKP SGNYNYLYRF LRKSKLKPFE RDISTEIYQV GNKPCNGVAG P NCYSPLQS YGFRPTYGVG HQPYRVVVLS FELLHAPATV CGP

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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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 252670
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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