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- EMDB-73430: Unbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down -

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Basic information

Entry
Database: EMDB / ID: EMD-73430
TitleUnbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down
Map dataUnbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down
Sample
  • Complex: Unbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down
    • Protein or peptide: SARS-CoV-2 LP.8.1 spike
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsWang Y / Hu Y / Chen Z / Liang B / 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
DepositionOct 19, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73430.png

Downloads & links

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Map

FileDownload / File: emd_73430.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 399.36 Å		0.83 Å/pix.
x 480 pix.
= 399.36 Å		0.83 Å/pix.
x 480 pix.
= 399.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.19496861 - 0.5759224
Average (Standard dev.)-0.00041080333 (±0.013226355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 399.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_73430_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_73430_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Unbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down

EntireName: Unbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down
Components
  • Complex: Unbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down
    • Protein or peptide: SARS-CoV-2 LP.8.1 spike

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Supramolecule #1: Unbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down

SupramoleculeName: Unbound SARS-CoV-2 LP.8.1 spike, 3-RBD-down / 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 LP.8.1 spike

MacromoleculeName: SARS-CoV-2 LP.8.1 spike / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVMPLF NLITTTQSYT NFTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVFIKVCE FQFCNDPFLD VYHKNNKSWM ESESGVYSSA NNCTFEYVSQ ...String:
MFVFLVLLPL VSSQCVMPLF NLITTTQSYT NFTRGVYYPD KVFRSSVLHL TQDLFLPFFS NVTWFHAISG TNGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVFIKVCE FQFCNDPFLD VYHKNNKSWM ESESGVYSSA NNCTFEYVSQ PFLMDLEGKQ GNLKNLSEFV FKNIDGYFKI YSKHTPIIGR DFPQGFSALE PLVDLPIGIN ITRFQTLLAL NRSYLTPGDS SSGWTAGAAD YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SIVRFPNVTN LCPFHEVFNA TTFASVYAWN RTRISNCVAD YSVLYNFAPF FAFKCYGVSP TKLNDLCFTN VYADSFVIKG NEVSQIAPGQ TGNIADYNYK LPDDFTGCVI AWNSNKLDSK RSGNYDYWYR SLRKSKLKPF ERDISTEIYQ AGNKPCKGKG PNCYFPLESY GFRPTYGVGH QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LTGTGVLTKS NKKFLPFQQF GRDIVDTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVSVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSRGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLFSTPSAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS VLNDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG RAHFPREGVF VSNGTHWFLT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQLEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQGSGYIPE APRDGQAYVR KDGEWVLLST FLGRSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK

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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

Concentration1.2 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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 10500
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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 62995
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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