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- EMDB-73395: BA.3.2.1 spike, flexible conformation -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73395
TitleBA.3.2.1 spike, flexible conformation
Map dataSARS-CoV-2 BA.3.2.1 spike, flexible conformation
Sample
  • Complex: SARS-CoV-2 BA.3.2 spike, flexible
    • Protein or peptide: SARS-CoV-2 BA.3.2 spike protein
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 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.3.2.1 spike, flexible conformation
Authors: Wang Y / Hu Y / Chen Z / Liang B / Xie X
History
DepositionOct 18, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73395.png

Downloads & links

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Map

FileDownload / File: emd_73395.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 BA.3.2.1 spike, flexible conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
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)

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-0.20680453 - 0.51069033
Average (Standard dev.)-0.00025147584 (±0.012372683)
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: Half Map A

Fileemd_73395_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_73395_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 : SARS-CoV-2 BA.3.2 spike, flexible

EntireName: SARS-CoV-2 BA.3.2 spike, flexible
Components
  • Complex: SARS-CoV-2 BA.3.2 spike, flexible
    • Protein or peptide: SARS-CoV-2 BA.3.2 spike protein

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Supramolecule #1: SARS-CoV-2 BA.3.2 spike, flexible

SupramoleculeName: SARS-CoV-2 BA.3.2 spike, flexible / 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 spike protein

MacromoleculeName: SARS-CoV-2 BA.3.2 spike protein / 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 DLICKQKFNG 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

Concentration1.2 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: 39.84 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 143152
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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