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- EMDB-62620: Cryo-EM structure of SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4 -

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Entry
Database: EMDB / ID: EMD-62620
TitleCryo-EM structure of SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4
Map data
Sample
  • Complex: SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4
    • Complex: SARS-CoV-2 BA.2 spike protein
      • Protein or peptide: Spike protein S1
    • Complex: ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Complex: The fragment of mAb 1C4
      • Protein or peptide: 1C4 light chain
      • Protein or peptide: 1C4 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Neutralizing antibody / Cryo-EM / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


ceramide biosynthetic process / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / transporter activator activity ...ceramide biosynthetic process / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / transporter activator activity / angiotensin maturation / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / metallopeptidase activity / virus receptor activity / regulation of inflammatory response / symbiont-mediated disruption of host tissue / endopeptidase activity / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / positive regulation of viral entry into host cell / membrane fusion / Attachment and Entry / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / 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 / cell surface / negative regulation of transcription by RNA polymerase II / : / membrane / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsSun H / Jiang Y / Li S / Zheng Q / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2025
Title: Engineering a multivalent antibody nanoparticle to overcome SARS-CoV-2 Omicron immune evasion.
Authors: Hui Sun / Yanan Jiang / Miaolin Lan / Ming Zhou / Gangshun Yi / Juan Shen / Tingting Deng / Liqin Liu / Yang Huang / Yu Li / Jinfu Su / Yanling Lin / Zhenqin Chen / Lizhi Zhou / Tingting Li ...Authors: Hui Sun / Yanan Jiang / Miaolin Lan / Ming Zhou / Gangshun Yi / Juan Shen / Tingting Deng / Liqin Liu / Yang Huang / Yu Li / Jinfu Su / Yanling Lin / Zhenqin Chen / Lizhi Zhou / Tingting Li / Hai Yu / Tong Cheng / Yali Zhang / Lunzhi Yuan / Shaowei Li / Ying Gu / Peijun Zhang / Ningshao Xia / Qingbing Zheng /
Abstract: The rapid evolution of SARS-CoV-2 and the subsequent emergence of Omicron subvariants pose significant challenges to the efficacy of existing vaccines and therapeutics, including those previously ...The rapid evolution of SARS-CoV-2 and the subsequent emergence of Omicron subvariants pose significant challenges to the efficacy of existing vaccines and therapeutics, including those previously reported most broad neutralizing antibodies (bnAbs). Here, we investigated the molecular basis of the altered neutralization profile of a bnAb, 1C4, against recent variants. 1C4 is effective against early variants from Alpha to Omicron BQ.1, but is circumvented by BQ.1.1, XBB and thereafter variants, primarily due to an additional R346T mutation that diminishes its binding affinity. Cryo-electron microscopy analysis revealed that despite the loss of neutralizing potency, 1C4 retained residual binding to the spike protein of immune-evasive variants such as XBB, which harbor altered receptor-binding domain (RBD). Furthermore, 1C4 exhibited a diminished capacity to inhibit ACE2 engagement with Omicron variants, amplifying the intricacies of viral immune evasion tactics. To address this, we employed the mi3-SpyCatcher-based nanoparticle to polymerize 1C4 (mi3-1C4), which reestablished the neutralization potency against recent variants by enhancing avidity via multivalent binding. Such multivalent binding can promote efficient spike aggregation as well as viral cross-linking, thereby providing enhanced protection against both the infection of Beta and XBB variants in a hamster model. Together, our findings delineate the molecular landscape of immune evasion by neutralizing antibodies and provide strategic insight for the adaptation of antibody engineering to keep pace with viral evolution.
History
DepositionDec 6, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62620.png

Downloads & links

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Map

FileDownload / File: emd_62620.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å		0.65 Å/pix.
x 360 pix.
= 234. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.001815023 - 2.0551827
Average (Standard dev.)0.0015688144 (±0.02843426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 233.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62620_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_62620_half_map_2.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4

EntireName: SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4
Components
  • Complex: SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4
    • Complex: SARS-CoV-2 BA.2 spike protein
      • Protein or peptide: Spike protein S1
    • Complex: ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Complex: The fragment of mAb 1C4
      • Protein or peptide: 1C4 light chain
      • Protein or peptide: 1C4 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4

SupramoleculeName: SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: SARS-CoV-2 BA.2 spike protein

SupramoleculeName: SARS-CoV-2 BA.2 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: ACE2

SupramoleculeName: ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: The fragment of mAb 1C4

SupramoleculeName: The fragment of mAb 1C4 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1
Details: Sequence reference for Homo sapiens (9606) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID Q56H28.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.344008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTEELAKTF LEKFNHEAEE LSYQSSLASW NYNTNITDEN VQKMNEAGAK WSAFYEEQSK LAKTYPLAEI HNTTVKRQLQ ALQQSGSSV LSADKSQRLN TILNAMSTIY STGKACNPNN PQECLLLEPG LDDIMENSKD YNERLWAWEG WRAEVGKQLR P LYEEYVAL ...String:
STTEELAKTF LEKFNHEAEE LSYQSSLASW NYNTNITDEN VQKMNEAGAK WSAFYEEQSK LAKTYPLAEI HNTTVKRQLQ ALQQSGSSV LSADKSQRLN TILNAMSTIY STGKACNPNN PQECLLLEPG LDDIMENSKD YNERLWAWEG WRAEVGKQLR P LYEEYVAL KNEMARANNY EDYGDYWRGD YEEEWTDGYN YSRSQLIKDV EHTFTQIKPL YQHLHAYVRA KLMDTYPSRI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTD AMVNQSWDAR RIFKEAEKFF VSVGLPNMTQ GFWENSMLTE PGD SRKVVC HPTAWDLGKG DFRIKMCTKV TMDDFLTAHH EMGHIQYDMA YAVQPFLLRN GANEGFHEAV GEIMSLSAAT PNHL KTIGL LSPGFSEDSE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKEQW MQKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVANDYSF IRYYTRTIYQ FQFQEALCRI AKHEGPLHKC DISNSSEAGK KLLQMLTLGK SKPWTLALEH VVGEKK MNV TPLLKYFEPL FTWLKEQN

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 21.026541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYN YKLPDDFTGC VIAWNSNNLD SKVGGNYNYL YRLFRKSNLK PFERDISTEI YQAGSTPCNG VEGFNCYFPL Q SYGFQPTN GVGYQPYRVV VLSFELVC

UniProtKB: Spike glycoprotein

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Macromolecule #3: 1C4 light chain

MacromoleculeName: 1C4 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.642854 KDa
SequenceString:
DIVLTQSPAT LSVTPGDNVS LSCRASQIIS NNLHWYQQKS HESPRLLIKY ASQSISGIPS RFSGSGSGTD FTLSINSVET EDFGMYFCQ QSNTWPLTCG SGTKLELN

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Macromolecule #4: 1C4 heavy chain

MacromoleculeName: 1C4 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.3849 KDa
SequenceString:
QIQLVQSGPE LKKPGETVKI SCKASGYTFT DYGLNWVKQA PGKGLKWMGW INTYSGEPTY NDEFRGRFAF SLETSTITAY LKINNLKNE DTATYFCARG GNWDWYFDVW GAGTTVTVSS

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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: 2 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182640
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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