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- EMDB-77348: Structure of BA.4-S-RBD/Ab#10-M30W-S94M -

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Basic information

Entry
Database: EMDB / ID: EMD-77348
TitleStructure of BA.4-S-RBD/Ab#10-M30W-S94M
Map data
Sample
  • Complex: Complex of SARS-CoV-2 Omicron BA.4 spike protein and Ab#10-M30W-S94M IgG
    • Protein or peptide: Ab#10-M30W-S94M heavy chain
    • Protein or peptide: Ab#10-M30W-S94M light chain
    • Protein or peptide: Spike protein
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDu J / Pallesen J
Funding support United States, 2 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Res Sq / Year: 2026
Title: Structure-Guided Design of Therapeutic Antibodies Targeting SARS-CoV-2 Omicron Variants.
Authors: Jesper Pallesen / Jianqiu Du / Yuanhan Wu / Sukanya Ghosh / Kelly Bayruns / Roopak Sadeesh / David Weiner
Abstract: The ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided ...The ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided computational design strategy to systematically optimize the COV2-2196 antibody for improved neutralization of Omicron variants. Through iterative rounds of computational design and experimental validation, we identified key paratope mutations that restored and enhanced antibody binding and neutralization potency against resistant viral strains. Cryo-EM structural analysis revealed the molecular basis for these improvements, highlighting how targeted modifications can accommodate epitope changes introduced by viral evolution. Our approach demonstrates that effective antibody optimization can be achieved using accessible computational resources, providing a practical framework for rapid therapeutic development. These findings underscore the potential of structure-based design to address challenges posed by viral antigenic drift and support the development of broadly effective antibody therapeutics for emerging infectious diseases.
History
DepositionMay 28, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77348.png

Downloads & links

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Map

FileDownload / File: emd_77348.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.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.16
Minimum - Maximum-0.1338873 - 12.549640999999999
Average (Standard dev.)-0.046737228 (±0.08078125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_77348_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77348_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of SARS-CoV-2 Omicron BA.4 spike protein and Ab#10-M30W-S...

EntireName: Complex of SARS-CoV-2 Omicron BA.4 spike protein and Ab#10-M30W-S94M IgG
Components
  • Complex: Complex of SARS-CoV-2 Omicron BA.4 spike protein and Ab#10-M30W-S94M IgG
    • Protein or peptide: Ab#10-M30W-S94M heavy chain
    • Protein or peptide: Ab#10-M30W-S94M light chain
    • Protein or peptide: Spike protein

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Supramolecule #1: Complex of SARS-CoV-2 Omicron BA.4 spike protein and Ab#10-M30W-S...

SupramoleculeName: Complex of SARS-CoV-2 Omicron BA.4 spike protein and Ab#10-M30W-S94M IgG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Ab#10-M30W-S94M heavy chain

MacromoleculeName: Ab#10-M30W-S94M heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.014645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDWTWRILFL VAAATGTHAQ MQLVQSGPEV KKPGTSVKVS CKASGFTFWS SAVQWVRQAR GQRLEWIGWI VIASGETNYA QKFQERVTI TRDMSTSTAY MELSSLRSED TAVYYCAAPY CSSRECNNGF DIWGQGTMVT VSSASTKGPS VFPLAPSSKS T SGGTAALG ...String:
MDWTWRILFL VAAATGTHAQ MQLVQSGPEV KKPGTSVKVS CKASGFTFWS SAVQWVRQAR GQRLEWIGWI VIASGETNYA QKFQERVTI TRDMSTSTAY MELSSLRSED TAVYYCAAPY CSSRECNNGF DIWGQGTMVT VSSASTKGPS VFPLAPSSKS T SGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KV EPKSCDK THTCPPCPAP ELLGGPSVFL FPPKPKDTLM ISRTPEVTCV VVDVSHEDPE VKFNWYVDGV EVHNAKTKPR EEQ YNSTYR VVSVLTVLHQ DWLNGKEYKC KVSNKALPAP IEKTISKAKG QPREPQVYTL PPSRDELTKN QVSLTCLVKG FYPS DIAVE WESNGQPENN YKTTPPVLDS DGSFFLYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPGK

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Macromolecule #2: Ab#10-M30W-S94M light chain

MacromoleculeName: Ab#10-M30W-S94M light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.939043 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLQTQVFIS LLLWISGAYG EIVLTQSPGT LSLSPGERAT LSCRASQSVS SMDLAWYQQK PGQAPRLLIY YASSRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QHYGGMRGWT FGQGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV ...String:
MVLQTQVFIS LLLWISGAYG EIVLTQSPGT LSLSPGERAT LSCRASQSVS SMDLAWYQQK PGQAPRLLIY YASSRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QHYGGMRGWT FGQGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS NTLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: Spike protein

MacromoleculeName: Spike protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron BA.4
Molecular weightTheoretical: 22.264092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIRGNEVSQ IAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDGKVSGN YNYRYRLFRK SNLKPFERDI STEIYQAGNK PCNGVAGVNC Y FPLQSYSF ...String:
PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIRGNEVSQ IAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDGKVSGN YNYRYRLFRK SNLKPFERDI STEIYQAGNK PCNGVAGVNC Y FPLQSYSF RPTYGVGHQP YRVVVLSFEL LHAPATVCG

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8d8q

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 536554
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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