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- EMDB-38790: BA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2) -

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Basic information

Entry
Database: EMDB / ID: EMD-38790
TitleBA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2)
Map data
Sample
  • Complex: BA.2.86 Spike in complex with 2 bovine ACE2
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein
KeywordsSARS-CoV-2 / complex / Spike / VIRAL PROTEIN
Function / homology
Function and homology information


angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / virus receptor activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release ...angiotensin-converting enzyme 2 / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / virus receptor activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / proteolysis / extracellular space / 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. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 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-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38790.png

Downloads & links

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Map

FileDownload / File: emd_38790.map.gz / Format: CCP4 / Size: 178 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 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å		1 Å/pix.
x 360 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.0981346 - 2.3978226
Average (Standard dev.)-0.0012722054 (±0.0662651)
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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Half map: #2

Fileemd_38790_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_38790_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 : BA.2.86 Spike in complex with 2 bovine ACE2

EntireName: BA.2.86 Spike in complex with 2 bovine ACE2
Components
  • Complex: BA.2.86 Spike in complex with 2 bovine ACE2
    • Protein or peptide: Processed angiotensin-converting enzyme 2
    • Protein or peptide: Spike glycoprotein

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Supramolecule #1: BA.2.86 Spike in complex with 2 bovine ACE2

SupramoleculeName: BA.2.86 Spike in complex with 2 bovine ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Processed angiotensin-converting enzyme 2

MacromoleculeName: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 69.701477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STTEEQAKTF LEKFNHEAED LSYQSSLASW NYNTNITDEN VQKMNEARAK WSAFYEEQSR MAKTYSLEEI QNLTLKRQLK ALQHSGTSA LSAEKSKRLN TILNKMSTIY STGKVLDPNT QECLALEPGL DDIMENSRDY NRRLWAWEGW RAEVGKQLRP L YEEYVVLE ...String:
STTEEQAKTF LEKFNHEAED LSYQSSLASW NYNTNITDEN VQKMNEARAK WSAFYEEQSR MAKTYSLEEI QNLTLKRQLK ALQHSGTSA LSAEKSKRLN TILNKMSTIY STGKVLDPNT QECLALEPGL DDIMENSRDY NRRLWAWEGW RAEVGKQLRP L YEEYVVLE NEMARANNYE DYGDYWRGDY EVTGAGDYDY SRDQLMKDVE RTFAEIKPLY EQLHAYVRAK LMHTYPSYIS PT GCLPAHL LGDMWGRFWT NLYSLTVPFE HKPSIDVTEK MENQSWDAER IFKEAEKFFV SISLPYMTQG FWDNSMLTEP GDG RKVVCH PTAWDLGKGD FRIKMCTKVT MDDFLTAHHE MGHIQYDMAY AAQPYLLRNG ANEGFHEAVG EIMSLSAATP HYLK ALGLL APDFHEDNET EINFLLKQAL TIVGTLPFTY MLEKWRWMVF KGEIPKQQWM EKWWEMKREI VGVVEPLPHD ETYCD PACL FHVAEDYSFI RYYTRTIYQF QFHEALCKTA KHEGALFKCD ISNSTEAGQR LLQMLRLGKS EPWTLALENI VGIKTM DVK PLLNYFEPLF TWLKEQNRNS FVGWSTEWTP YSD

UniProtKB: Angiotensin-converting enzyme 2

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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: 124.478305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TTTQSYTNSF TRGVYYPDKV FRSSVLHLTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLD SKTQSLLIVN NATNVFIKVC EFQFCNDPFL GVYYHKNNKS WMESEFGVYS SANNCTFEYV SQPFLMDLEG K QGNFKNLR ...String:
TTTQSYTNSF TRGVYYPDKV FRSSVLHLTQ DLFLPFFSNV TWFHAIHVSG TNGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLD SKTQSLLIVN NATNVFIKVC EFQFCNDPFL GVYYHKNNKS WMESEFGVYS SANNCTFEYV SQPFLMDLEG K QGNFKNLR EFVFKNIDGY FKIYSKHTPI IGRDFPQGFS ALEPLVDLPI GINITRFQTL LALNRSYLTP GDSSSGWTAG AA DYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPTESIVRFP NVTNLCPFHE VFN ATRFAS VYAWNRTRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIKGNEVSQ IAPGQTGNIA DYNY KLPDD FTGCVIAWNS NKLDSKHSGN YDYWYRLFRK SKLKPFERDI STEIYQAGNK PCKGKGPNCY FPLQSYGFRP TYGVG HQPY RVVVLSFELL HAPATVCGPK KSTNLVKNKC VNFNFNGLTG TGVLTKSNKK FLPFQQFGRD IVDTTDAVRD PQTLEI LDI TPCSFGGVSV ITPGTNTSNQ VAVLYQGVNC TEVSVAIHAD QLTPTWRVYS TGSNVFQTRA GCLIGAEYVN NSYECDI PI GAGICASYQT QTNSPRRARS VASQSIIAYT MSLGAENSVA YSNNSIAIPT NFTISVTTEI LPVSMTKTSV DCTMYICG D STECSNLLLQ YGSFCTQLKR ALTGIAVEQD KNTQEVFAQV KQIYKTPPIK YFGGFNFSQI LPDPSKPSKR SPIEDLLFN KVTLADAGFI KQYGDCLGDI AARDLICAQK FNGLTVLPPL LTDEMIAQYT SALLAGTITS GWTFGAGPAL QIPFPMQMAY RFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLFSTPS ALGKLQDVVN HNAQALNTLV KQLSSKFGAI SSVLNDILSR L DPPEAEVQ IDRLITGRLQ SLQTYVTQQL IRAAEIRASA NLAATKMSEC VLGQSKRVDF CGKGYHLMSF PQSAPHGVVF LH VTYVPAQ EKNFTTAPAI CHDGKAHFPR EGVFVSNGTH WFVTQRNFYE PQIITTDNTF VSGNCDVVIG IVNNTVYDPL QLE

UniProtKB: Spike glycoprotein

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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 TECNAI 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5828
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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