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- EMDB-38201: Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with ACE2 -

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Basic information

Entry
Database: EMDB / ID: EMD-38201
TitleCryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with ACE2
Map data
Sample
  • Complex: SARS-CoV-2 S-BQ.1 and ACE2 complex
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Angiotensin-converting enzyme 2,Green fluorescent protein (Fragment)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsspike protein / VIRAL PROTEIN
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / receptor-mediated endocytosis of virus by host cell / carboxypeptidase activity / Attachment and Entry / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / bioluminescence / blood vessel diameter maintenance / generation of precursor metabolites and energy / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / negative regulation of ERK1 and ERK2 cascade / cilium / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / host cell surface / Virion Assembly and Release / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Neutral zinc metallopeptidases, zinc-binding region signature. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Green fluorescent protein / Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Aequorea victoria (jellyfish)
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 4, 2023-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38201.png

Downloads & links

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Map

FileDownload / File: emd_38201.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.12765905 - 2.8134186
Average (Standard dev.)0.0032568378 (±0.036158867)
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: #1

Fileemd_38201_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_38201_half_map_2.map
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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
    • Protein or peptide: Angiotensin-converting enzyme 2,Green fluorescent protein (Fragment)
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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: #1-#2
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: 142.010484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVLP FNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN N CTFEYVSQ ...String:
MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAISGTNG TKRFDNPVLP FNDGVYFAS TEKSNIIRGW IFGTTLDSKT QSLLIVNNAT NVVIKVCEFQ FCNDPFLDVY YHKNNKSWME SEFRVYSSAN N CTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLG RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LH RSYLTPG DSSSGWTAGA AAYYVGYLQP RTFLLKYNEN GTITDAVDCA LDPLSETKCT LKSFTVEKGI YQTSNFRVQP TES IVRFPN ITNLCPFDEV FNATRFASVY AWNRKRISNC VADYSVLYNF APFFAFKCYG VSPTKLNDLC FTNVYADSFV IRGN EVSQI APGQTGNIAD YNYKLPDDFT GCVIAWNSNK LDSTVGGNYN YRYRLFRKSK LKPFERDIST EIYQAGNKPC NGVAG VNCY FPLQSYGFRP TYGVGHQPYR VVVLSFELLH APATVCGPKK STNLVKNKCV NFNFNGLTGT GVLTESNKKF LPFQQF GRD IADTTDAVRD PQTLEILDIT PCSFGGVSVI TPGTNTSNQV AVLYQGVNCT EVPVAIHADQ LTPTWRVYST GSNVFQT RA GCLIGAEYVN NSYECDIPIG AGICASYQTQ TKSHGSASSV ASQSIIAYTM SLGAENSVAY SNNSIAIPTN FTISVTTE I LPVSMTKTSV DCTMYICGDS TECSNLLLQY GSFCTQLKRA LTGIAVEQDK NTQEVFAQVK QIYKTPPIKY FGGFNFSQI LPDPSKPSKR SPIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF KGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGPAL QIPFPMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTPSA LGKLQDVVNH NAQALNTLVK Q LSSKFGAI SSVLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GK GYHLMSF PQSAPHGVVF LHVTYVPAQE KNFTTAPAIC HDGKAHFPRE GVFVSNGTHW FVTQRNFYEP QIITTDNTFV SGN CDVVIG IVNNTVYDPL QPELDSFKEE LDKYFKNHTS PDVDLGDISG INASVVNIQK EIDRLNEVAK NLNESLIDLQ ELGK YEQEF GSGGYIPEAP RDGQAYVRKD GEWVLLSTFL KGQDNSADIQ HSGRPLESRG PFEQKLISEE DLNMHTGHHH HHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: Angiotensin-converting enzyme 2,Green fluorescent protein (Fragment)

MacromoleculeName: Angiotensin-converting enzyme 2,Green fluorescent protein (Fragment)
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 98.273477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSSSWLLLS LVAVTAAQST IEEQAKTFLD KFNHEAEDLF YQSSLASWNY NTNITEENVQ NMNNAGDKWS AFLKEQSTLA QMYPLQEIQ NLTVKLQLQA LQQNGSSVLS EDKSKRLNTI LNTMSTIYST GKVCNPDNPQ ECLLLEPGLN EIMANSLDYN E RLWAWESW ...String:
MSSSSWLLLS LVAVTAAQST IEEQAKTFLD KFNHEAEDLF YQSSLASWNY NTNITEENVQ NMNNAGDKWS AFLKEQSTLA QMYPLQEIQ NLTVKLQLQA LQQNGSSVLS EDKSKRLNTI LNTMSTIYST GKVCNPDNPQ ECLLLEPGLN EIMANSLDYN E RLWAWESW RSEVGKQLRP LYEEYVVLKN EMARANHYED YGDYWRGDYE VNGVDGYDYS RGQLIEDVEH TFEEIKPLYE HL HAYVRAK LMNAYPSYIS PIGCLPAHLL GDMWGRFWTN LYSLTVPFGQ KPNIDVTDAM VDQAWDAQRI FKEAEKFFVS VGL PNMTQG FWENSMLTDP GNVQKAVCHP TAWDLGKGDF RILMCTKVTM DDFLTAHHEM GHIQYDMAYA AQPFLLRNGA NEGF HEAVG EIMSLSAATP KHLKSIGLLS PDFQEDNETE INFLLKQALT IVGTLPFTYM LEKWRWMVFK GEIPKDQWMK KWWEM KREI VGVVEPVPHD ETYCDPASLF HVSNDYSFIR YYTRTLYQFQ FQEALCQAAK HEGPLHKCDI SNSTEAGQKL FNMLRL GKS EPWTLALENV VGAKNMNVRP LLNYFEPLFT WLKDQNKNSF VGWSTDWSPY ADGSGGSGSG GSKGEELFTG VVPILVE LD GDVNGHKFSV RGEGEGDATN GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK RHDFFKSAMP EGYVQERT I SFKDDGTYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNFNSH NVYITADKQK NGIKANFKIR HNVEDGSVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSVL SKDPNEKRDH MVLLEFVTAA GITHGMDELY K

UniProtKB: Angiotensin-converting enzyme 2, Green fluorescent protein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 31 / 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

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

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
Output model

PDB-8xal:
Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with ACE2

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