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- EMDB-73523: Cryo-EM structure of BA.5 spike, Open conformation -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73523
TitleCryo-EM structure of BA.5 spike, Open conformation
Map dataunsharpened map of BA.5 spike, open conformation
Sample
  • Complex: BA.5 spike
    • Protein or peptide: Spike glycoprotein
KeywordsSARS-CoV-2 / entry / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsYe G / Bu F / Li F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI171954 United States
CitationJournal: To Be Published
Title: A SARS-CoV-2 entry inhibitor trimerizes to lock the spike trimer in its closed conformation
Authors: Mou H / Gao B / Ye G / Bu F / Zhang L / Farzan M / Li F / Choe H
History
DepositionOct 23, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73523.png

Downloads & links

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Map

FileDownload / File: emd_73523.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map of BA.5 spike, open conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 390 pix.
= 345.28 Å		0.89 Å/pix.
x 390 pix.
= 345.28 Å		0.89 Å/pix.
x 390 pix.
= 345.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.19313408 - 0.4821129
Average (Standard dev.)0.0002175837 (±0.013084594)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions390390390
Spacing390390390
CellA=B=C: 345.27988 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map of BA.5 spike, open conformation

Fileemd_73523_additional_1.map
Annotationsharpened map of BA.5 spike, open conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A map of BA.5 spike, open conformation

Fileemd_73523_half_map_1.map
Annotationhalf_A map of BA.5 spike, open conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B map of BA.5 spike, open conformation

Fileemd_73523_half_map_2.map
Annotationhalf_B map of BA.5 spike, open conformation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BA.5 spike

EntireName: BA.5 spike
Components
  • Complex: BA.5 spike
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: BA.5 spike

SupramoleculeName: BA.5 spike / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 139.006469 KDa
Recombinant expressionOrganism: Homo (humans)
SequenceString: MDAMKRGLCC VLLLCGAVFV SASQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME S EFRVYSSA ...String:
MDAMKRGLCC VLLLCGAVFV SASQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVL PFNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME S EFRVYSSA NNCTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLG RDLPQGFSAL EPLVDLPIGI NI TRFQTLL ALHRSYLTPG DSSSGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQT SNFRVQ PTESIVRFPN ITNLCPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNV YADSF VIRGNEVSQI APGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSKVGGNYN YRYRLFRKSN LKPFERDIST EIYQA GNKP CNGVAGVNCY FPLQSYGFRP TYGVGHQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLTGT GVLTES NKK FLPFQQFGRD IADTTDAVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVPVAIHADQ LTPTWRV YS TGSNVFQTRA GCLIGAEYVN NSYECDIPIG AGICASYQTQ TKSHAGARSV ASQSIIAYTM SLGAENSVAY SNNSIAIP T NFTISVTTEI LPVSMTKTSV DCTMYICGDS TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIK YFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITS GWTFGAGPAL QIPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNH N AQALNTLV KQLSSKFGAI SSVLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LG QSKRVDF CGKGYHLMSF PQSAPHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QII TTDNTF VSGNCDVVIG IVNNTVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNE SLIDL QELGKYEQYI KGSGYIPEAP RDGQAYVRKD GEWVLLSTFL GHHHHHH

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 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: PDB ENTRY
PDB model - PDB ID:

8cin

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 64086
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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