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- EMDB-39422: STA map of C3 symmetry spike protein from active SARS-CoV-2 vririons -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-39422
TitleSTA map of C3 symmetry spike protein from active SARS-CoV-2 vririons
Map data
Sample
  • Virus: Severe acute respiratory syndrome coronavirus 2
    • Protein or peptide: SARS-CoV-2 Spike protein
Keywordsvirions / spike protein / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 14.3 Å
AuthorsDokainish HM / Maenaka K
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101093 Japan
Japan Agency for Medical Research and Development (AMED)JP20ae0101047 Japan
Japan Agency for Medical Research and Development (AMED)JP21fk0108463 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121037 Japan
Japan Agency for Medical Research and Development (AMED)JP223fa627005 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
Japan Science and TechnologyJPMJCR20H8 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP20H05873 Japan
CitationJournal: To Be Published
Title: Unprecedented spike flexibility revealed by BSL3 Cryo-ET of active SARS-CoV-2 virions
Authors: Dokainish HM / Fukuhara H / Maenaka K
History
DepositionMar 11, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39422.png

Downloads & links

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Map

FileDownload / File: emd_39422.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.88 Å/pix.
x 144 pix.
= 271.296 Å		1.88 Å/pix.
x 144 pix.
= 271.296 Å		1.88 Å/pix.
x 144 pix.
= 271.296 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.884 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.75
Minimum - Maximum-3.5068357 - 10.916169999999999
Average (Standard dev.)0.03317533 (±1.195578)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 271.296 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39422_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39422_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39422_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 : Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2
Components
  • Virus: Severe acute respiratory syndrome coronavirus 2
    • Protein or peptide: SARS-CoV-2 Spike protein

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2697049
Sci species name: Severe acute respiratory syndrome coronavirus 2
Sci species strain: Wuhan / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: VeroE6/TMPRSS2

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Macromolecule #1: SARS-CoV-2 Spike protein

MacromoleculeName: SARS-CoV-2 Spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Wuhan
SequenceString: MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIH VSGTNGTKRF DNPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI V NNATNVVI KVCEFQFCND PFLGVYYHKN NKSWMESEFR VYSSANNCTF ...String:
MFVFLVLLPL VSSQCVNLTT RTQLPPAYTN SFTRGVYYPD KVFRSSVLHS TQDLFLPFFS NVTWFHAIH VSGTNGTKRF DNPVLPFNDG VYFASTEKSN IIRGWIFGTT LDSKTQSLLI V NNATNVVI KVCEFQFCND PFLGVYYHKN NKSWMESEFR VYSSANNCTF EYVSQPFLMD LE GKQGNFK NLREFVFKNI DGYFKIYSKH TPINLVRDLP QGFSALEPLV DLPIGINITR FQT LLALHR SYLTPGDSSS GWTAGAAAYY VGYLQPRTFL LKYNENGTIT DAVDCALDPL SETK CTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPFGEVFNAT RFASVYAWNR KRISN CVAD YSVLYNSASF STFKCYGVSP TKLNDLCFTN VYADSFVIRG DEVRQIAPGQ TGKIAD YNY KLPDDFTGCV IAWNSNNLDS KVGGNYNYLY RLFRKSNLKP FERDISTEIY QAGSTPC NG VEGFNCYFPL QSYGFQPTNG VGYQPYRVVV LSFELLHAPA TVCGPKKSTN LVKNKCVN F NFNGLTGTGV LTESNKKFLP FQQFGRDIAD TTDAVRDPQT LEILDITPCS FGGVSVITP GTNTSNQVAV LYQDVNCTEV PVAIHADQLT PTWRVYSTGS NVFQTRAGCL IGAEHVNNSY ECDIPIGAG ICASYQTQTN SPRRARSVAS QSIIAYTMSL GAENSVAYSN NSIAIPTNFT I SVTTEILP VSMTKTSVDC TMYICGDSTE CSNLLLQYGS FCTQLNRALT GIAVEQDKNT QE VFAQVKQ IYKTPPIKDF GGFNFSQILP DPSKPSKRSF IEDLLFNKVT LADAGFIKQY GDC LGDIAA RDLICAQKFN GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGAALQI PFAM QMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTASAL GKLQDVVNQN AQALN TLVK QLSSNFGAIS SVLNDILSRL DKVEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRA SAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HVTYVPAQEK NFTTAPA IC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGNCDVVIGI VNNTVYDP L QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDL QELGKYEQYI KWPWYIWLGF IAGLIAIVMV TIMLCCMTSC CSCLKGCCSC GSCCKFDEDD SEPVLKGVK LHYT

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: Opti-MEM
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 291 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 0.73 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.2 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 14.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 237
ExtractionNumber tomograms: 42 / Number images used: 237 / Method: manual / Software - Name: RELION (ver. 4.0)
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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