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- EMDB-75887: SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH -

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Basic information

Entry
Database: EMDB / ID: EMD-75887
TitleSARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH
Map datasharpened map
Sample
  • Complex: SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH
    • Protein or peptide: SARS-CoV-2 Omicron BA.4 spike protein
    • Protein or peptide: Omi32 heavy chain
    • Protein or peptide: Omi32 light chain
    • Protein or peptide: LC-Kappa VHH
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody / rbd / omicron / ba.4 / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKang G / Phillips AM / Catalano C / Scapin G
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2026
Title: Biophysical trade-offs in antibody evolution are resolved by conformation-mediated epistasis.
Authors: Cole R Tharp / Claudio Catalano / Anthony Khalifeh / Sam Ghaffari-Kashani / Ruimin Huang / Gyunghoon Kang / Giovanna Scapin / Angela M Phillips /
Abstract: Protein evolution is constrained by multidimensional biophysical factors, in which mutations that enhance one property often compromise another. Antibodies represent an extreme case: they evolve ...Protein evolution is constrained by multidimensional biophysical factors, in which mutations that enhance one property often compromise another. Antibodies represent an extreme case: they evolve rapidly to bind diverse antigens, yet mutations that improve affinity can disrupt folding, reduce cell-surface trafficking, or promote self-reactivity, and are typically selected against during affinity maturation. Though biophysical characterization of individual antibodies suggests that such trade-offs are pervasive, their impact on antibody evolutionary trajectories remains unclear, in part because existing high-throughput biophysical methods rely on heterologous systems that are often poorly suited for human proteins. Here, we develop a high-throughput platform to quantify multiple biophysical parameters of large libraries of full-length proteins that are natively synthesized, processed, and displayed on human cells. We apply this approach to a human antibody lineage that matures to recognize divergent SARS-CoV-2 variants by measuring the surface expression, antigen affinity, and self-reactivity for all 2 possible evolutionary intermediates between the unmutated and mature sequences. These measurements reveal that mutations differentially affect these biophysical properties - in some cases, improving one property at the expense of another. We leverage these data to compute the likelihood of all possible evolutionary paths, finding that very few paths can navigate these multidimensional requirements. The few accessible paths acquire mutations in a specific order that either circumvent trade-offs between biophysical properties or offset deleterious effects on one property with beneficial effects on another. By determining the structures of the ancestral and evolved antibodies, we find that these coordinated mutational effects arise from a conformational rearrangement that alleviates steric clashes and reshapes the biophysical landscape, enabling otherwise inaccessible mutational paths. Together, this work defines the multidimensional biophysical constraints and structural mechanisms that govern antibody evolution and establishes a general framework for mapping and predicting the biophysical effects of mutations in human proteins.
History
DepositionMar 6, 2026-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75887.png

Downloads & links

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Map

FileDownload / File: emd_75887.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 440 pix.
= 411.84 Å		0.94 Å/pix.
x 440 pix.
= 411.84 Å		0.94 Å/pix.
x 440 pix.
= 411.84 Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.936 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.35180345 - 0.54240996
Average (Standard dev.)-0.000060040915 (±0.007932894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 411.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_75887_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half Map A

Fileemd_75887_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_75887_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH

EntireName: SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH
Components
  • Complex: SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH
    • Protein or peptide: SARS-CoV-2 Omicron BA.4 spike protein
    • Protein or peptide: Omi32 heavy chain
    • Protein or peptide: Omi32 light chain
    • Protein or peptide: LC-Kappa VHH
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH

SupramoleculeName: SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 Fab and LC-Kappa VHH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SARS-CoV-2 Omicron BA.4 spike protein

MacromoleculeName: SARS-CoV-2 Omicron BA.4 spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 22.315162 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHTNLCPFDE VFNATRFASV YAWNRKRISN CVADYSVLYN FAPFFAFKCY GVSPTKLNDL CFTNVYADSF VIRGNEVSQI APGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKVGGNY NYRYRLFRKS NLKPFERDIS TEIYQAGNKP CNGVAGVNCY F PLQSYGFR ...String:
HHTNLCPFDE VFNATRFASV YAWNRKRISN CVADYSVLYN FAPFFAFKCY GVSPTKLNDL CFTNVYADSF VIRGNEVSQI APGQTGNIA DYNYKLPDDF TGCVIAWNSN KLDSKVGGNY NYRYRLFRKS NLKPFERDIS TEIYQAGNKP CNGVAGVNCY F PLQSYGFR PTYGVGHQPY RVVVLSFELL HAPATVCGK

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Macromolecule #2: Omi32 heavy chain

MacromoleculeName: Omi32 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.277039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG VVQPGRSLRL SCAASGFTFS NYGMHWVRQA PGKGLEWVAV YWYDGGNKFY ADSVKGRFTI SRDNSKNTLY LQMNSLRVE DTAVYYCARD TAPPDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
EVQLVESGGG VVQPGRSLRL SCAASGFTFS NYGMHWVRQA PGKGLEWVAV YWYDGGNKFY ADSVKGRFTI SRDNSKNTLY LQMNSLRVE DTAVYYCARD TAPPDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPK

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Macromolecule #3: Omi32 light chain

MacromoleculeName: Omi32 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.476111 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AIRMTQSPGT LSLSPGERAT LSCRASQSIS SSFLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGTSPRLT FGGGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
AIRMTQSPGT LSLSPGERAT LSCRASQSIS SSFLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGTSPRLT FGGGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #4: LC-Kappa VHH

MacromoleculeName: LC-Kappa VHH / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.162396 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
EVQLQESGGG LVQPGGSLRL SCAASGRTIS RYAMSWFRQA PGKEREFVAT ARRSGDGAFY ADSVQGRFTV SRDDAKNTVY LQMNSLKPE DTAVYYCAID SDTFYSGSYD YWGQGTQVTV S

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 25.05 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 106182
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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