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- EMDB-76849: Cryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with K852A mutatio... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-76849
TitleCryo-EM structure of SARS-CoV-2 BA.3.2.1 spike with K852A mutation, open 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: To Be Published
Title: Functional and Structural Basis of Omicron BA.3.2.1 Spike
Authors: Wang Y / Hu Y / Chen Z / Zou J / Zhang K / Ren P / Shi PY / Liang B / Xie X
History
DepositionApr 21, 2026-
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_76849.png

Downloads & links

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Map

FileDownload / File: emd_76849.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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-0.25716114 - 0.6334485
Average (Standard dev.)-0.00013997877 (±0.01655652)
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_76849_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_76849_half_map_2.map
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.3.2.1 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 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
200.0 mMNaClsodium chloride
20.0 mMTristris (hydroxymethyl) aminomethane
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.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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