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- EMDB-73599: Local refinement of BA.3.2 spike (3-RBD-down), RBD-A, RBD-C and NTD-B -

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Basic information

Entry
Database: EMDB / ID: EMD-73599
TitleLocal refinement of BA.3.2 spike (3-RBD-down), RBD-A, RBD-C and NTD-B
Map dataLocal refinement of BA.3.2.1 spike (3-RBD-down), RBD-A, RBD-C and NTD-B
Sample
  • Complex: SARS-CoV-2 BA.3.2.1 spike
    • Protein or peptide: SARS-CoV-2 BA.3.2.1 spike
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 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 26, 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_73599.png

Downloads & links

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Map

FileDownload / File: emd_73599.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement of BA.3.2.1 spike (3-RBD-down), RBD-A, RBD-C and NTD-B
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: 0.14
Minimum - Maximum-0.27415186 - 0.6802999
Average (Standard dev.)-0.00006758628 (±0.013062094)
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 B

Fileemd_73599_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_73599_half_map_2.map
AnnotationHalf Map A
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

EntireName: SARS-CoV-2 BA.3.2.1 spike
Components
  • Complex: SARS-CoV-2 BA.3.2.1 spike
    • Protein or peptide: SARS-CoV-2 BA.3.2.1 spike
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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

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

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

MacromoleculeName: SARS-CoV-2 BA.3.2.1 spike / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 139.346641 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLLL VSSQCVNLTT TTQLPLAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNIT RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFNNKSWM ESESRVYSSA KNCTFEYVFQ P FLMDLEGK ...String:
MFVFLVLLLL VSSQCVNLTT TTQLPLAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHVISG TNGTKRFDNP VLPFNDGVY FASIEKSNIT RGWIFGTTLD SKTQSLLIVN NATNVVIKVC EFQFNNKSWM ESESRVYSSA KNCTFEYVFQ P FLMDLEGK QGNFTNLREF VFKNIDGYFK IYSKHTPIIV RDLPQGFSAL EPLVDLPIGI NITRFQTLLH RSYLTSGDSS SG WTAGAAA YYVGYLQPRT FLLKYNENGT ITDAVDCALD PLSETKCTLK SFTVEKGIYQ TSNFRVQPTE SVVRFPNITN LCP FYEVFN ATRFPSVYAW NRKRISNCVA DYSVLYNFAP FFTFKCYGVS PTKLNDLCFT NVYADSFVIK GNEVSQIAPG QTGN IADYN YKLPDDFTGC VISWNSNRLD SKADGNYNYW YRLFRKSKLK PFERDISTEI YQAGNNPCNG VKGFNCYFPL QSYSF RPTY GVGYQPYRVV VLSFELLHAP ATVCGPKNST NLVKNKCVNF NFNGLTGTGV LTDSNKKFLP FQQFGRDIAD TTDAVR DPQ TLDILDITPC SFGGVSVITP GTNTSNQVAV LYQGVNCTEV PVAIRADQLT PTWRVYSTGS KGFQTRAGCL IGAKYVN NS YECDIPIGAG ICASYQTQTR SRGSASSVDS QSIIAYTMSL GAENLVAYSN NSIAIPTNFT ISVTTEILPV SMTKTSVD C TMYICGDSTE CSNLLLQYGS FCTQLKRALT GIAVEQDKNT QEVFAQVKQI YKTPPITYFG GFNFSQILPD PSKPSKRSP IEDLLFNKVT LADAGFIKQY GDCLGDIAAR DLICKQKFNG LTVLPPLLTD EMIAQYTSAL LAGTITSGWT FGAGPALQIP FPMQMAYRF NGIGVTQNVL YENQKLIANQ FNSAIGKIQD SLFSTPSALG KLQDVVNHNA QALNTLVKQL SSKFGAISSV L NDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS AP HGVVFLH VTYVPAQEKN FTTAPAICHD GKAHFPREGV FVSNGTHWFV TQRNFYEPQI ITTDNTFVSG NCDVVIGIVN NTV YDPLQP ELDSFKEELD KYFKNHTSRD VDLGDISGIN ASVVNIQKEI ERLNEVAKNL NESLIDLQEL GKYEQGSGYI PEAP RDGQA YVRKDGEWVL LSTFLGRSLE VLFQGPGHHH HHHHHSAWSH PQFEK

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 673009
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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