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- EMDB-38789: BA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2) -

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Basic information

Entry
Database: EMDB / ID: EMD-38789
TitleBA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2)
Map data
Sample
  • Complex: BA.2.86 Spike in complex with bovine ACE2
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / complex / Spike / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / proteolysis / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
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. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsYue C / Liu P
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: BA.2.86 Spike in complex with bovine ACE2
Authors: Yue C / Liu P
History
DepositionJan 21, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_38789.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.6304746 - 1.6351008
Average (Standard dev.)-0.0014973978 (±0.057247546)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : BA.2.86 Spike in complex with bovine ACE2

EntireName: BA.2.86 Spike in complex with bovine ACE2
Components
  • Complex: BA.2.86 Spike in complex with bovine ACE2
    • Protein or peptide: Spike glycoprotein
    • Protein or peptide: Angiotensin-converting enzyme
  • Ligand: ZINC ION
  • Ligand: CHLORIDE ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BA.2.86 Spike in complex with bovine ACE2

SupramoleculeName: BA.2.86 Spike in complex with bovine ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Angiotensin-converting enzyme

MacromoleculeName: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases)
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 93.201109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTGSFWLLLS LVAVTAAQST TEEQAKTFLE KFNHEAEDLS YQSSLASWNY NTNITDENVQ KMNEARAKWS AFYEEQSRMA KTYSLEEIQ NLTLKRQLKA LQHSGTSALS AEKSKRLNTI LNKMSTIYST GKVLDPNTQE CLALEPGLDD IMENSRDYNR R LWAWEGWR ...String:
MTGSFWLLLS LVAVTAAQST TEEQAKTFLE KFNHEAEDLS YQSSLASWNY NTNITDENVQ KMNEARAKWS AFYEEQSRMA KTYSLEEIQ NLTLKRQLKA LQHSGTSALS AEKSKRLNTI LNKMSTIYST GKVLDPNTQE CLALEPGLDD IMENSRDYNR R LWAWEGWR AEVGKQLRPL YEEYVVLENE MARANNYEDY GDYWRGDYEV TGAGDYDYSR DQLMKDVERT FAEIKPLYEQ LH AYVRAKL MHTYPSYISP TGCLPAHLLG DMWGRFWTNL YSLTVPFEHK PSIDVTEKME NQSWDAERIF KEAEKFFVSI SLP YMTQGF WDNSMLTEPG DGRKVVCHPT AWDLGKGDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAA QPYLLRNGAN EGFH EAVGE IMSLSAATPH YLKALGLLAP DFHEDNETEI NFLLKQALTI VGTLPFTYML EKWRWMVFKG EIPKQQWMEK WWEMK REIV GVVEPLPHDE TYCDPACLFH VAEDYSFIRY YTRTIYQFQF HEALCKTAKH EGALFKCDIS NSTEAGQRLL QMLRLG KSE PWTLALENIV GIKTMDVKPL LNYFEPLFTW LKEQNRNSFV GWSTEWTPYS DQSIKVRISL KSALGENAYE WNDNEMY LF QSSVAYAMRK YFSEARNETV LFGEDNVWVS DKKPRISFKF FVTSPNNVSD IIPRTEVENA IRLSRDRFND VFQLDDNS L EFLGIQPTLG PPYEPPVTIW LIIFGVVMGV VVIGIVVLIF TGIRNRRKKN QASSEENPYG SVDLNKGENN SGFQNIDDV QTSL

UniProtKB: Angiotensin-converting enzyme

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Macromolecule #2: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron/BA.2.86
Molecular weightTheoretical: 134.041156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ATMFVFLVLL PLVSSQCVMP LFNLITTTQS YTNSFTRGVY YPDKVFRSSV LHLTQDLFLP FFSNVTWFHA ISGTNGTKRF DNPVLPFND GVYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNATNVFI KVCEFQFCND PFLDVYHKNN KSWMESESGV Y SSANNCTF ...String:
ATMFVFLVLL PLVSSQCVMP LFNLITTTQS YTNSFTRGVY YPDKVFRSSV LHLTQDLFLP FFSNVTWFHA ISGTNGTKRF DNPVLPFND GVYFASTEKS NIIRGWIFGT TLDSKTQSLL IVNNATNVFI KVCEFQFCND PFLDVYHKNN KSWMESESGV Y SSANNCTF EYVSQPFLMD LEGKQGNFKN LREFVFKNID GYFKIYSKHT PIIGRDFPQG FSALEPLVDL PIGINITRFQ TL LALNRSY LTPGDSSSGW TAGAADYYVG YLQPRTFLLK YNENGTITDA VDCALDPLSE TKCTLKSFTV EKGIYQTSNF RVQ PTESIV RFPNVTNLCP FHEVFNATRF ASVYAWNRTR ISNCVADYSV LYNFAPFFAF KCYGVSPTKL NDLCFTNVYA DSFV IKGNE VSQIAPGQTG NIADYNYKLP DDFTGCVIAW NSNKLDSKHS GNYDYWYRLF RKSKLKPFER DISTEIYQAG NKPCK GKGP NCYFPLQSYG FRPTYGVGHQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNFNFNGL TGTGVLTKSN KKFLPF QQF GRDIVDTTDA VRDPQTLEIL DITPCSFGGV SVITPGTNTS NQVAVLYQGV NCTEVSVAIH ADQLTPTWRV YSTGSNV FQ TRAGCLIGAE YVNNSYECDI PIGAGICASY QTQTKSRRAA ASVASQSIIA YTMSLGAENS VAYSNNSIAI PTNFTISV T TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL KRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKYFGGFNF SQILPDPSKP SKRSPIEDLL FNKVTLADAG FIKQYGDCLG DIAARDLICA QKFNGLTVLP PLLTDEMIAQ YTSALLAGTI TSGWTFGAG PALQIPFPMQ MAYRFNGIGV TQNVLYENQK LIANQFNSAI GKIQDSLFST PSALGKLQDV VNHNAQALNT L VKQLSSKF GAISSVLNDI LSRLDPPEAE VQIDRLITGR LQSLQTYVTQ QLIRAAEIRA SANLAATKMS ECVLGQSKRV DF CGKGYHL MSFPQSAPHG VVFLHVTYVP AQEKNFTTAP AICHDGKAHF PREGVFVSNG THWFVTQRNF YEPQIITTDN TFV SGNCDV VIGIVNNTVY DPLQLELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQE LGKYE Q

UniProtKB: Spike glycoprotein

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 36 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89392
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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