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- EMDB-75891: SARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab an... -

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Basic information

Entry
Database: EMDB / ID: EMD-75891
TitleSARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab and LC-Kappa VHH
Map dataSARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab and LC-Kappa VHH
Sample
  • Complex: SARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab and LC-Kappa VHH
    • Protein or peptide: SARS-CoV-2 Omicron BA.1 spike protein
    • Protein or peptide: Omi32 germline heavy chain
    • Protein or peptide: LC-Kappa VHH
    • Protein or peptide: Omi32 germline light chain
Keywordsgermline / antibody / rbd / omicron / ba.1 / IMMUNE SYSTEM / IMMUNE SYSTEM-Viral Protein complex
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 / 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_75891.png

Downloads & links

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Map

FileDownload / File: emd_75891.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab and LC-Kappa VHH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 440 pix.
= 405.24 Å		0.92 Å/pix.
x 440 pix.
= 405.24 Å		0.92 Å/pix.
x 440 pix.
= 405.24 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0881
Minimum - Maximum-0.28908396 - 0.44174337
Average (Standard dev.)-0.00009522287 (±0.00906603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 405.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened full map

Fileemd_75891_additional_1.map
Annotationunsharpened full map
Projections & Slices
AxesZYX

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Half map: half map B

Fileemd_75891_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_75891_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab an...

EntireName: SARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab and LC-Kappa VHH
Components
  • Complex: SARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab and LC-Kappa VHH
    • Protein or peptide: SARS-CoV-2 Omicron BA.1 spike protein
    • Protein or peptide: Omi32 germline heavy chain
    • Protein or peptide: LC-Kappa VHH
    • Protein or peptide: Omi32 germline light chain

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Supramolecule #1: SARS-CoV-2 Omicron BA.1 RBD in complex with Omi32 germline Fab an...

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

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

MacromoleculeName: SARS-CoV-2 Omicron BA.1 spike protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 20.890547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CPFDEVFNAT RFASVYAWNR KRISNCVADY SVLYNLAPFF TFKCYGVSPT KLNDLCFTNV YADSFVIRGD EVRQIAPGQT GNIADYNYK LPDDFTGCVI AWNSNKLDSK VSGNYNYLYR LFRKSNLKPF ERDISTEIYQ AGNKPCNGVA GFNCYFPLRS Y SFRPTYGV GHQPYRVVVL SFEL

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Macromolecule #2: Omi32 germline heavy chain

MacromoleculeName: Omi32 germline heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.188969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYGMHWVRQA PGKGLEWVAV IWYDGSNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD TAPPDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String:
QVQLVESGGG VVQPGRSLRL SCAASGFTFS SYGMHWVRQA PGKGLEWVAV IWYDGSNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD TAPPDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPK

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Macromolecule #3: LC-Kappa VHH

MacromoleculeName: LC-Kappa VHH / type: protein_or_peptide / ID: 3 / 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 #4: Omi32 germline light chain

MacromoleculeName: Omi32 germline light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.460018 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSPRLT FGGGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSPRLT FGGGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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: 24.85 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: 47421
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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