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- EMDB-62810: Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with ACE2 const... -

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Basic information

Entry
Database: EMDB / ID: EMD-62810
TitleCryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with ACE2 constituent map 2
Map data
Sample
  • Complex: SARS-CoV-2 S-BQ.1 and ACE2 complex
    • Protein or peptide: Spike glycoprotein
Keywordsspike protein / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / Resolution: 3.2 Å
AuthorsHsu HF / Wu MH / Chang YC / Hsu STD
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IDR-112-04 Taiwan
Academia Sinica (Taiwan)AS-CDA-109-L08 Taiwan
CitationJournal: JCI Insight / Year: 2024
Title: Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody.
Authors: Yi-Hsuan Chang / Min-Feng Hsu / Wei-Nan Chen / Min-Hao Wu / Wye-Lup Kong / Mei-Yeh Jade Lu / Chih-Heng Huang / Fang-Ju Chang / Lan-Yi Chang / Ho-Yang Tsai / Chao-Ping Tung / Jou-Hui Yu / ...Authors: Yi-Hsuan Chang / Min-Feng Hsu / Wei-Nan Chen / Min-Hao Wu / Wye-Lup Kong / Mei-Yeh Jade Lu / Chih-Heng Huang / Fang-Ju Chang / Lan-Yi Chang / Ho-Yang Tsai / Chao-Ping Tung / Jou-Hui Yu / Yali Kuo / Yu-Chi Chou / Li-Yang Bai / Yuan-Chih Chang / An-Yu Chen / Cheng-Cheung Chen / Yi-Hua Chen / Chun-Che Liao / Chih-Shin Chang / Jian-Jong Liang / Yi-Ling Lin / Takashi Angata / Shang-Te Danny Hsu / Kuo-I Lin /
Abstract: Since its emergence, SARS-CoV-2 has been continuously evolving, hampering the effectiveness of current vaccines against COVID-19. mAbs can be used to treat patients at risk of severe COVID-19. Thus, ...Since its emergence, SARS-CoV-2 has been continuously evolving, hampering the effectiveness of current vaccines against COVID-19. mAbs can be used to treat patients at risk of severe COVID-19. Thus, the development of broadly protective mAbs and an understanding of the underlying protective mechanisms are of great importance. Here, we isolated mAbs from donors with breakthrough infection with Omicron subvariants using a single-B cell screening platform. We identified a mAb, O5C2, which possesses broad-spectrum neutralization and antibody-dependent cell-mediated cytotoxic activities against SARS-CoV-2 variants, including EG.5.1. Single-particle analysis by cryo-electron microscopy revealed that O5C2 targeted an unusually large epitope within the receptor-binding domain of spike protein that overlapped with the angiotensin-converting enzyme 2 binding interface. Furthermore, O5C2 effectively protected against BA.5 Omicron infection in vivo by mediating changes in transcriptomes enriched in genes involved in apoptosis and interferon responses. Our findings provide insights into the development of pan-protective mAbs against SARS-CoV-2.
History
DepositionDec 20, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62810.png

Downloads & links

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Map

FileDownload / File: emd_62810.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 460 pix.
= 496.8 Å		1.08 Å/pix.
x 460 pix.
= 496.8 Å		1.08 Å/pix.
x 460 pix.
= 496.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.8917024 - 2.1451647
Average (Standard dev.)-0.0003781859 (±0.033776533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 496.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62810_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_62810_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 S-BQ.1 and ACE2 complex

EntireName: SARS-CoV-2 S-BQ.1 and ACE2 complex
Components
  • Complex: SARS-CoV-2 S-BQ.1 and ACE2 complex
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: SARS-CoV-2 S-BQ.1 and ACE2 complex

SupramoleculeName: SARS-CoV-2 S-BQ.1 and ACE2 complex / 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 / Enantiomer: LEVO
SequenceString: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLDVYY HKNNKSWMES EFRVYSSANN CTFEYVSQPF ...String:
MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVLP FNDGVYFAST EKSNIIRGWI FGTTLDSKTQ SLLIVNNATN VVIKVCEFQF CNDPFLDVYY HKNNKSWMES EFRVYSSANN CTFEYVSQPF LMDLEGKQGN FKNLREFVFK NIDGYFKIYS KHTPINLGRD LPQGFSALEP LVDLPIGINI TRFQTLLALH RSYLTPGDSS SGWTAGAAAY YVGYLQPRTF LLKYNENGTI TDAVDCALDP LSETKCTLKS FTVEKGIYQT SNFRVQPTES IVRFPNITNL CPFDEVFNAT RFASVYAWNR KRISNCVADY SVLYNFAPFF AFKCYGVSPT KLNDLCFTNV YADSFVIRGN EVSQIAPGQT GNIADYNYKL PDDFTGCVIA WNSNKLDSTV GGNYNYRYRL FRKSKLKPFE RDISTEIYQA GNKPCNGVAG VNCYFPLQSY GFRPTYGVGH QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LTGTGVLTES NKKFLPFQQF GRDIADTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVPVAIH ADQLTPTWRV YSTGSNVFQT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVTTE ILPVSMTKTS VDCTMYICGD STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF KGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPALQ IPFPMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTPSAL GKLQDVVNHN AQALNTLVKQ LSSKFGAISS VLNDILSRLD PPEAEVQIDR LITGRLQSLQ TYVTQQLIRA AEIRASANLA ATKMSECVLG QSKRVDFCGK GYHLMSFPQS APHGVVFLHV TYVPAQEKNF TTAPAICHDG KAHFPREGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGDISGINAS VVNIQKEIDR LNEVAKNLNE SLIDLQELGK YEQEFGSGGY IPEAPRDGQA YVRKDGEWVL LSTFLKGQDN SADIQHSGRP LESRGPFEQK LISEEDLNMH TGHHHHHH

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8dm5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 128951
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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