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- EMDB-66671: Local refinement of SARS-CoV-2 KP.3.1.1 RBD with BD57-2704 and AB... -

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Basic information

Entry
Database: EMDB / ID: EMD-66671
TitleLocal refinement of SARS-CoV-2 KP.3.1.1 RBD with BD57-2704 and AB2-122 Fab
Map data
Sample
  • Complex: BD57-2704_AB2-122_KP.3.1.1 RBD
    • Protein or peptide: BD57-2704 heavy chain
    • Protein or peptide: BD57-2704 light chain
    • Protein or peptide: AB2-122 heavy chain
    • Protein or peptide: AB2-122 light chain
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / antibody / fab / STRUCTURAL PROTEIN / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsCao YL / Wang YX
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Recurrent SARS-CoV-2 Omicron broadly neutralizing humanized antibodies in different single human V1-2-rearranging mouse models.
Authors: Himanshu Batra / Sai Luo / Kevin O Saunders / Jaclyn S Higgins / Fanchong Jian / Jun Zhang / Md Golam Kibria / G M Jonaid / Qingchen J Zhou / Amanda Eaton / Kenneth Cronin / Michael L ...Authors: Himanshu Batra / Sai Luo / Kevin O Saunders / Jaclyn S Higgins / Fanchong Jian / Jun Zhang / Md Golam Kibria / G M Jonaid / Qingchen J Zhou / Amanda Eaton / Kenneth Cronin / Michael L Mallory / Melissa Mattocks / Robert J Edwards / Robert Parks / Esther M Lee / Adam Yongxin Ye / Aimee Chapdelaine Williams / Geeyoun Jung / Katayoun Mansouri / S Munir Alam / David C Montefiori / Ming Tian / Ralph S Baric / Yunlong Cao / Barton F Haynes / Bing Chen / Frederick W Alt /
Abstract: During V(D)J recombination, antibody diversity is enhanced by nontemplated junctional modifications that generate immensely diverse heavy chain (HC) and light chain (LC) complementarity-determining 3 ...During V(D)J recombination, antibody diversity is enhanced by nontemplated junctional modifications that generate immensely diverse heavy chain (HC) and light chain (LC) complementarity-determining 3 antigen-contact regions (CDR3s). We previously developed a mouse model that generates diverse antibody repertoires by rearranging a single human V1-2 and Vκ1-33, associated with highly diverse CDR3s generated by V(D)J recombination with mouse Ds and/or Js. Immunization of this model with SARS-CoV-2 D614G spike elicited an antibody that potently neutralized SARS-CoV-2 variants through Omicron BA.2.754. Here, we report a related mouse model in which a single V1-2 rearranges to human D3-3 and J6, generating diverse HC-CDR3s much longer on average than those of our prior model. Omicron BA.4/.5 spike-ferritin nanoparticle-immunization of the new model elicited four highly related humanized antibodies that potently neutralize downstream Omicron subvariants. All four antibodies had 12 AA HC-CDR3s with two aromatic amino acids that engage an epitope comprising a hydrophobic patch opened-up by early Omicron lineage mutations and conserved in subsequent variants. Immunization of our prior, shorter CDR3-based model, elicited slightly less potent neutralizing antibodies that bound the same Omicron epitope, and were similar in all other aspects to those from the long, fully human CDR3 model. One tested antibody from each set reduced lung viral titers in a mouse-adapted BQ1.1 challenge. The antibodies we describe are related in their epitope recognition to recently described antibodies from Omicron-infected humans. These studies validate the utility of single human V- and Vκ-rearranging mice for discovering humanized antibodies that neutralize emerging pathogens.
History
DepositionOct 21, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66671.png

Downloads & links

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Map

FileDownload / File: emd_66671.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 440 pix.
= 418. Å		0.95 Å/pix.
x 440 pix.
= 418. Å		0.95 Å/pix.
x 440 pix.
= 418. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.151
Minimum - Maximum-1.0308826 - 1.3401952
Average (Standard dev.)-0.0004849451 (±0.017914651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 418.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66671_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_66671_additional_1.map
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Half map: #1

Fileemd_66671_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_66671_half_map_2.map
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Sample components

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Entire : BD57-2704_AB2-122_KP.3.1.1 RBD

EntireName: BD57-2704_AB2-122_KP.3.1.1 RBD
Components
  • Complex: BD57-2704_AB2-122_KP.3.1.1 RBD
    • Protein or peptide: BD57-2704 heavy chain
    • Protein or peptide: BD57-2704 light chain
    • Protein or peptide: AB2-122 heavy chain
    • Protein or peptide: AB2-122 light chain
    • Protein or peptide: Spike protein S1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BD57-2704_AB2-122_KP.3.1.1 RBD

SupramoleculeName: BD57-2704_AB2-122_KP.3.1.1 RBD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: BD57-2704 heavy chain

MacromoleculeName: BD57-2704 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.691178 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGG LIQPGGSLRL SCVASEIIVS ANYMTWVRQA PGKGLEWVSV LFAGGTTYYA DSVKGRCTIS RDNSKNTLYL EMNSLRADD TAVYYCARSL EELGGFDSWG QGTLVTVSS

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Macromolecule #2: BD57-2704 light chain

MacromoleculeName: BD57-2704 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.506897 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EILMTQSPAT LSVSLGARAT LSCRATPSIG TNVAWYQQKP GQAPRLLLFG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYNNGPPYAF GQGTKLEIK

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Macromolecule #3: AB2-122 heavy chain

MacromoleculeName: AB2-122 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.274907 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYYLYWVRQA PGQGLEWMGW INPKTGGTNY AQKFQGRVTM TRDTSISTAY MELNRLSSD DTAVYYCGRR DFWSHYMDVW GKGTTVTVS

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Macromolecule #4: AB2-122 light chain

MacromoleculeName: AB2-122 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.75493 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
DIQMTQSPSS LSASVGDRVA ITCQASQDIY NNLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTISSLQP EDIATYFCQ QYDYLSWTFG GGTKLEIK

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Macromolecule #5: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: KP.3.1.1
Molecular weightTheoretical: 20.951584 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NLCPFHEVFN ATRFASVYAW NRTRISNCVA DYSVLYNFAP FFAFKCYGVS PTKLNDLCFT NVYADSFVIK GNEVSQIAPG QTGNIADYN YKLPDDFTGC VIAWNSNKLD SKHSGNYDYW YRSLRKSKLK PFERDISTEI YQAGNKPCKG KGPNCYFPLE S YGFRPTYG VGHQPYRVVV LSFEL

UniProtKB: Spike glycoprotein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / 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

Concentration1 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / 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: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: CCP4 package / Number images used: 196773
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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