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- EMDB-37725: Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (... -

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Basic information

Entry
Database: EMDB / ID: EMD-37725
TitleCryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
    • Complex: fab
      • Protein or peptide: S309 fab heavy chain
      • Protein or peptide: S309 fab light chain
      • Protein or peptide: CB6 fab mutant heavy chain
      • Protein or peptide: CB6 fab mutant light chain
      • Protein or peptide: S304 fab heavy chain
      • Protein or peptide: S304 fab light chain
    • Complex: SARS-CoV-2 XBB.1.5 RBD
      • Protein or peptide: Spike protein S1
KeywordsSARS-CoV-2 / XBB.1.5 / RBD / CB6 / receptor-binding domain / etesevimab / mutant / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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-related coronavirus / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsSu C / Qi JX / Gao GF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Hlife / Year: 2025
Title: Enabling the immune escaped etesevimab fully-armed against SARS-CoV-2 Omicron subvariants including KP.2
Authors: Su C / He J / Xie Y / Hu Y / Li X / Qiao S / Liu P / Huang M / Zhang R / Wang L / Chang Z / Sun W / Xu K / Zhang J / Cao L / Han P / Zhao X / Qi J / Wang Q / Yang M / Gao GF
History
DepositionOct 10, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37725.png

Downloads & links

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Map

FileDownload / File: emd_37725.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.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0023
Minimum - Maximum-0.0017737707 - 1.585122
Average (Standard dev.)0.00070439954 (±0.018138511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37725_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37725_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 : Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (...

EntireName: Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
    • Complex: fab
      • Protein or peptide: S309 fab heavy chain
      • Protein or peptide: S309 fab light chain
      • Protein or peptide: CB6 fab mutant heavy chain
      • Protein or peptide: CB6 fab mutant light chain
      • Protein or peptide: S304 fab heavy chain
      • Protein or peptide: S304 fab light chain
    • Complex: SARS-CoV-2 XBB.1.5 RBD
      • Protein or peptide: Spike protein S1

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: fab

SupramoleculeName: fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus

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Supramolecule #3: SARS-CoV-2 XBB.1.5 RBD

SupramoleculeName: SARS-CoV-2 XBB.1.5 RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7

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Macromolecule #1: S309 fab heavy chain

MacromoleculeName: S309 fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.747725 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYPFT SYGISWVRQA PGQGLEWMGW ISTYNGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD YTRGAWFGES LIGGFDNWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYPFT SYGISWVRQA PGQGLEWMGW ISTYNGNTNY AQKFQGRVTM TTDTSTTTGY MELRRLRSD DTAVYYCARD YTRGAWFGES LIGGFDNWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDKTHHHHH H

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Macromolecule #2: S309 fab light chain

MacromoleculeName: S309 fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.291777 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPGT LSLSPGERAT LSCRASQTVS STSLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQHDTSLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPGT LSLSPGERAT LSCRASQTVS STSLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC QQHDTSLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGECS

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Macromolecule #3: CB6 fab mutant heavy chain

MacromoleculeName: CB6 fab mutant heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.862912 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASEFIVS YNYMSWVRQA PGKGLEWVSV IYPGGSTFYA DSVKGRFTIS RDNSMNTLFL QMNSLRAED TAVYYCARVL PINGYYLDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
EVQLVESGGG LVQPGGSLRL SCAASEFIVS YNYMSWVRQA PGKGLEWVSV IYPGGSTFYA DSVKGRFTIS RDNSMNTLFL QMNSLRAED TAVYYCARVL PINGYYLDYW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSCDKTHHH HHH

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Macromolecule #4: CB6 fab mutant light chain

MacromoleculeName: CB6 fab mutant light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.559068 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPSS LSASVGDRVT ITCRASQSIA YYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSSDPPEYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIVMTQSPSS LSASVGDRVT ITCRASQSIA YYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QSSDPPEYTF GQGTKLEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGECS

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Macromolecule #5: S304 fab heavy chain

MacromoleculeName: S304 fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.93067 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG LVQPGGSLRL SCAASGFTFS SYDMHWVRQT TGKGLEWVST IGTAGDTYYP DSVKGRFTIS REDAKNSLYL QMNSLRAGD TAVYYCARGD SSGYYYYFDY WGQGTLLTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QVQLVESGGG LVQPGGSLRL SCAASGFTFS SYDMHWVRQT TGKGLEWVST IGTAGDTYYP DSVKGRFTIS REDAKNSLYL QMNSLRAGD TAVYYCARGD SSGYYYYFDY WGQGTLLTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSCDKTHH HHHH

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Macromolecule #6: S304 fab light chain

MacromoleculeName: S304 fab light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.457025 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSAAVGDRVT ITCRASQSIG SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFAIYYCQ QSYVSPTYTF GPGTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSAAVGDRVT ITCRASQSIG SYLNWYQQKP GKAPKLLIYA ASSLQSGVPS RFSGSGSGTD FTLTISSLQP EDFAIYYCQ QSYVSPTYTF GPGTKVDIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGECS

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Macromolecule #7: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 7 / Details: XBB.1.5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 25.988436 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF HEVFNATTFA SVYAWNRKRI SNCVADYSVI YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVIRGNEV SQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKPSG NYNYLYRLFR KSKLKPFERD ISTEIYQAGN K PCNGVAGP ...String:
RVQPTESIVR FPNITNLCPF HEVFNATTFA SVYAWNRKRI SNCVADYSVI YNFAPFFAFK CYGVSPTKLN DLCFTNVYAD SFVIRGNEV SQIAPGQTGN IADYNYKLPD DFTGCVIAWN SNKLDSKPSG NYNYLYRLFR KSKLKPFERD ISTEIYQAGN K PCNGVAGP NCYSPLQSYG FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFHHHHH H

UniProtKB: Spike glycoprotein

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7jw0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 282682
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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