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- EMDB-73439: Unbound LP.8.1 spike, 1-RBD-up -

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Basic information

Entry
Database: EMDB / ID: EMD-73439
TitleUnbound LP.8.1 spike, 1-RBD-up
Map dataUnbound LP.8.1 spike, 1-RBD-up
Sample
  • Complex: Unbound SARS-CoV-2 LP.8.1 spike, 1-RBD-up
    • 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: 2.81 Å
AuthorsWang Y / Hu Y / Chen Z / Liang B / Xie X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural characteristics of the SARS-CoV-2 Omicron subvariant BA.3.2 and LP.8.1 spike protein
Authors: Wang Y / Hu Y / Chen Z / Liang B / Xie X
History
DepositionOct 19, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73439.png

Downloads & links

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Map

FileDownload / File: emd_73439.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnbound LP.8.1 spike, 1-RBD-up
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: 0.09
Minimum - Maximum-0.21421963 - 0.62892574
Average (Standard dev.)-0.00029141744 (±0.013025939)
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_73439_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_73439_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, 1-RBD-up

EntireName: Unbound SARS-CoV-2 LP.8.1 spike, 1-RBD-up
Components
  • Complex: Unbound SARS-CoV-2 LP.8.1 spike, 1-RBD-up
    • Protein or peptide: SARS-CoV-2 LP.8.1 spike

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

SupramoleculeName: Unbound SARS-CoV-2 LP.8.1 spike, 1-RBD-up / 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: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 228395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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