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- EMDB-48151: Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion... -

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Basic information

Entry
Database: EMDB / ID: EMD-48151
TitleCryo-EM structure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (one RBD up state)
Map datastructure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (one RBD up state)
Sample
  • Complex: SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / COVID-19 / Spike / VIRAL PROTEIN
Function / homology
Function and homology information


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 / 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 / host cell plasma membrane / virion membrane ...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 / 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 / host cell plasma membrane / virion membrane / identical protein binding / 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 speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsFeng Z / Huang J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Cell Rep / Year: 2025
Title: Structural and functional insights into the evolution of SARS-CoV-2 KP.3.1.1 spike protein.
Authors: Ziqi Feng / Jiachen Huang / Sabyasachi Baboo / Jolene K Diedrich / Sandhya Bangaru / James C Paulson / John R Yates / Meng Yuan / Ian A Wilson / Andrew B Ward /
Abstract: The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigate how mutations and a deletion in the ...The JN.1-sublineage KP.3.1.1 recently emerged as the globally prevalent SARS-CoV-2 variant, demonstrating increased infectivity and antibody escape. We investigate how mutations and a deletion in the KP.3.1.1 spike protein (S) affect hACE2 binding and antibody escape. Mass spectrometry confirms a new glycan site at residue N30 that alters the glycoforms at neighboring N61. Cryoelectron microscopy (cryo-EM) structures show that the N30 glycan and rearrangement of adjacent residues do not significantly change the overall spike structure, up-down ratio of receptor-binding domains (RBDs), or hACE2 binding. Furthermore, a KP.3.1.1 S with hACE2 structure further confirms an epistatic effect between F456L and Q493E on hACE2 binding. Our analysis shows that SARS-CoV-2 variants that emerged after late 2023 are now incorporating reversions to residues found in other sarbecoviruses, including the N30 glycan, Q493E, and others. Overall, these results inform on the structural and functional consequences of the KP.3.1.1 mutations, the current SARS-CoV-2 evolutionary trajectory, and immune evasion.
History
DepositionDec 4, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48151.png

Downloads & links

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Map

FileDownload / File: emd_48151.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein (one RBD up state)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6087502 - 0.92312694
Average (Standard dev.)-0.00024274187 (±0.019681929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48151_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half Map B

Fileemd_48151_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48151_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein

EntireName: SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein
Components
  • Complex: SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein

SupramoleculeName: SARS-CoV-2 Omicron JN.1.11+Q493E+S31deletion spike protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 133.214031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLIT TTQSYTNFTR GVYYPDKVFR SSVLHLTQDL FLPFFSNVTW FHAISGTNGT KRFDNPVLPF NDGVYFAST EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VFIKVCEFQF CNDPFLDVYH KNNKSWMESE SGVYSSANNC T FEYVSQPF ...String:
MFVFLVLLPL VSSQCVNLIT TTQSYTNFTR GVYYPDKVFR SSVLHLTQDL FLPFFSNVTW FHAISGTNGT KRFDNPVLPF NDGVYFAST EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VFIKVCEFQF CNDPFLDVYH KNNKSWMESE SGVYSSANNC T FEYVSQPF LMDLEGKQGN FKNLREFVFK NIDGYFKIYS KHTPIIGRDF PQGFSALEPL VDLPIGINIT RFQTLLALNR SY LTPGDSS SGWTAGAADY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVR FPNVTN LCPFHEVFNA TRFASVYAWN RTRISNCVAD YSVLYNFAPF FAFKCYGVSP TKLNDLCFTN VYADSFVIKG NEVS QIAPG QTGNIADYNY KLPDDFTGCV IAWNSNKLDS KHSGNYDYWY RSFRKSKLKP FERDISTEIY QAGNKPCKGK GPNCY FPLE SYGFRPTYGV GHQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLTGTGVLT KSNKKFLPFQ QFGRDI VDT TDAVRDPQTL EILDITPCSF GGVSVITPGT NTSNQVAVLY QGVNCTEVSV AIHADQLTPT WRVYSTGSNV FQTRAGC LI GAEYVNNSYE CDIPIGAGIC ASYQTQTKSR GSASSVASQS IIAYTMSLGA ENSVAYSNNS IAIPTNFTIS VTTEILPV S MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLKRALTGI AVEQDKNTQE VFAQVKQIYK TPPIKYFGGF NFSQILPDP SKPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL ICAQKFNGLT VLPPLLTDEM IAQYTSALLA GTITSGWTFG AGPALQIPF PMQMAYRFNG IGVTQNVLYE NQKLIANQFN SAIGKIQDSL FSTPSALGKL QDVVNHNAQA LNTLVKQLSS K FGAISSVL NDILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KRVDFCGKGY HL MSFPQSA PHGVVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREGVFV SNGTHWFLTQ RNFYEPQIIT TDNTFVSGNC DVV IGIVNN TVYDPLQLEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQ

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 22 / 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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 44.84 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8y5j

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94590
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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