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- EMDB-48147: Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in... -

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Entry
Database: EMDB / ID: EMD-48147
TitleCryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human ACE2
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human ACE2
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / COVID-19 / Spike / hACE2 / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of amino acid transport / 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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy ...positive regulation of amino acid transport / 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 / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / viral life cycle / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / 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 / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / 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 / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / 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 / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
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. / 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
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 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) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48147.png

Downloads & links

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Map

FileDownload / File: emd_48147.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 600 pix.
= 430.8 Å		0.72 Å/pix.
x 600 pix.
= 430.8 Å		0.72 Å/pix.
x 600 pix.
= 430.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.702351 - 1.1203967
Average (Standard dev.)-0.00013715115 (±0.018003443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 430.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48147_msk_1.map
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Half map: #2

Fileemd_48147_half_map_1.map
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Half map: #1

Fileemd_48147_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in...

EntireName: Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human ACE2
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human ACE2
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.982562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL ...String:
STIEEQAKTF LDKFNHEAED LFYQSSLASW NYNTNITEEN VQNMNNAGDK WSAFLKEQST LAQMYPLQEI QNLTVKLQLQ ALQQNGSSV LSEDKSKRLN TILNTMSTIY STGKVCNPDN PQECLLLEPG LNEIMANSLD YNERLWAWES WRSEVGKQLR P LYEEYVVL KNEMARANHY EDYGDYWRGD YEVNGVDGYD YSRGQLIEDV EHTFEEIKPL YEHLHAYVRA KLMNAYPSYI SP IGCLPAH LLGDMWGRFW TNLYSLTVPF GQKPNIDVTD AMVDQAWDAQ RIFKEAEKFF VSVGLPNMTQ GFWENSMLTD PGN VQKAVC HPTAWDLGKG DFRILMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LSPDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKDQW MKKWWEMKRE IVGVVEPVPH DETYC DPAS LFHVSNDYSF IRYYTRTLYQ FQFQEALCQA AKHEGPLHKC DISNSTEAGQ KLFNMLRLGK SEPWTLALEN VVGAKN MNV RPLLNYFEPL FTWLKDQNKN SFVGWSTDWS PYADHHHHHH

UniProtKB: Angiotensin-converting enzyme 2

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron KP.3.1.1
Molecular weightTheoretical: 133.180016 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 RSLRKSKLKP 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 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 26 / 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:

7a97

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131224
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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