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- EMDB-76694: Cryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with K852A mutatio... -

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Basic information

Entry
Database: EMDB / ID: EMD-76694
TitleCryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with K852A mutation, flexible conformation
Map data
Sample
  • Complex: SARS-CoV-2 BA.3.2.1 spike with K852A mutation
    • Protein or peptide: SARS-CoV-2 BA.3.2.1 spike with K852A mutation
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsWang Y / Hu Y / Xie X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2026
Title: Functional and structural basis of Omicron BA.3.2.1 spike.
Authors: Yan Wang / Yanping Hu / Zhenhang Chen / Jing Zou / Ke Zhang / Ping Ren / Pei-Yong Shi / Bo Liang / Xuping Xie /
Abstract: SARS-CoV-2 BA.3.2 sublineages, derived from BA.3 and carrying substantial spike divergence, raised concerns about altered fitness and antigenicity. Using BA.3.2.1 as a representative strain, we ...SARS-CoV-2 BA.3.2 sublineages, derived from BA.3 and carrying substantial spike divergence, raised concerns about altered fitness and antigenicity. Using BA.3.2.1 as a representative strain, we engineered live-attenuated SARS-CoV-2 encoding BA.3.2.1, LP.8.1, or XEC spikes and benchmarked them against BA.3 and KP.3. BA.3.2.1 outcompetes BA.3 in primary human airway epithelium but replicates less efficiently than JN.1 descendants and shows the greatest resistance to neutralization by KP.2/KP.3 convalescent sera. Although BA.3.2.1 RBD binds hACE2 with high affinity, its trimeric spike engages hACE2 less efficiently than LP.8.1. Cryoelectron microscopy structures reveal that BA.3.2.1 spike predominantly adopts a compact, asymmetric closed conformation stabilized by protomer rearrangements, N-linked glycosylation, and a distinct fusion-peptide-proximal region. This architecture increases spike stability, limits receptor engagement, reduces fusogenicity, and masks antibody-sensitive epitopes. Thus, BA.3.2.1 enhances immune evasion at the cost of replication fitness, providing a structural-functional explanation for BA.3.2's limited prevalence and underscoring the need for continued variant surveillance.
History
DepositionApr 15, 2026-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76694.png

Downloads & links

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Map

FileDownload / File: emd_76694.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 416 pix.
= 346.112 Å		0.83 Å/pix.
x 416 pix.
= 346.112 Å		0.83 Å/pix.
x 416 pix.
= 346.112 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.2591047 - 0.6082614
Average (Standard dev.)-0.000119104916 (±0.015062504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 346.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_76694_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_76694_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 BA.3.2.1 spike with K852A mutation

EntireName: SARS-CoV-2 BA.3.2.1 spike with K852A mutation
Components
  • Complex: SARS-CoV-2 BA.3.2.1 spike with K852A mutation
    • Protein or peptide: SARS-CoV-2 BA.3.2.1 spike with K852A mutation

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Supramolecule #1: SARS-CoV-2 BA.3.2.1 spike with K852A mutation

SupramoleculeName: SARS-CoV-2 BA.3.2.1 spike with K852A mutation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: SARS-CoV-2 BA.3.2.1 spike with K852A mutation

MacromoleculeName: SARS-CoV-2 BA.3.2.1 spike with K852A mutation / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLLL VSSQCVNLTT TTQLPLAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVYF ASIEKSNITR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFNNKSWME SESRVYSSAK NCTFEYVFQP FLMDLEGKQG ...String:
MFVFLVLLLL VSSQCVNLTT TTQLPLAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVYF ASIEKSNITR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFNNKSWME SESRVYSSAK NCTFEYVFQP FLMDLEGKQG NFTNLREFVF KNIDGYFKIY SKHTPIIVRD LPQGFSALEP LVDLPIGINI TRFQTLLHRS YLTSGDSSSG WTAGAAAYYV GYLQPRTFLL KYNENGTITD AVDCALDPLS ETKCTLKSFT VEKGIYQTSN FRVQPTESVV RFPNITNLCP FYEVFNATRF PSVYAWNRKR ISNCVADYSV LYNFAPFFTF KCYGVSPTKL NDLCFTNVYA DSFVIKGNEV SQIAPGQTGN IADYNYKLPD DFTGCVISWN SNRLDSKADG NYNYWYRLFR KSKLKPFERD ISTEIYQAGN NPCNGVKGFN CYFPLQSYSF RPTYGVGYQP YRVVVLSFEL LHAPATVCGP KNSTNLVKNK CVNFNFNGLT GTGVLTDSNK KFLPFQQFGR DIADTTDAVR DPQTLDILDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVPVAIRAD QLTPTWRVYS TGSKGFQTRA GCLIGAKYVN NSYECDIPIG AGICASYQTQ TRSRGSASSV DSQSIIAYTM SLGAENLVAY SNNSIAIPTN FTISVTTEIL PVSMTKTSVD CTMYICGDST ECSNLLLQYG SFCTQLKRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPITYF GGFNFSQILP DPSKPSKRSP IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICAQKFNG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGPALQIP FPMQMAYRFN GIGVTQNVLY ENQKLIANQF NSAIGKIQDS LFSTPSALGK LQDVVNHNAQ ALNTLVKQLS SKFGAISSVL NDILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECVLGQS KRVDFCGKGY HLMSFPQSAP HGVVFLHVTY VPAQEKNFTT APAICHDGKA HFPREGVFVS NGTHWFVTQR NFYEPQIITT DNTFVSGNCD VVIGIVNNTV YDPLQPELDS FKEELDKYFK NHTSRDVDLG DISGINASVV NIQKEIERLN EVAKNLNESL IDLQELGKYE QGSGYIPEAP RDGQAYVRKD GEWVLLSTFL GRSLEVLFQG PGHHHHHHHH SAWSHPQFEK GGGSGGGGSG GSAWSHPQFE K

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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

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTristris (hydroxymethyl) aminomethane
200.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 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: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 128756
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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