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- EMDB-15591: BA.2.12.1 SARS-CoV-2 Spike bound to mouse ACE2 (local) -

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Entry
Database: EMDB / ID: EMD-15591
TitleBA.2.12.1 SARS-CoV-2 Spike bound to mouse ACE2 (local)
Map datab2
Sample
  • Complex: SARS-COV2 BA.2.12.1 bound to mouse ACE2
    • Complex: SARS-CoV-2 BA.2.12.1 spike protein
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: Mouse ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2,Ig gamma-2A chain C region, membrane-bound form
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-COV2 / omicron / Spike / RBD / mouse / ACE2 / ANTIVIRAL PROTEIN / BA2.12.1 / VIRAL PROTEIN
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / positive regulation of B cell activation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment ...Metabolism of Angiotensinogen to Angiotensins / positive regulation of B cell activation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / endosome to lysosome transport / immunoglobulin complex, circulating / immunoglobulin receptor binding / angiotensin-converting enzyme 2 / antigen processing and presentation / positive regulation of L-proline import across plasma membrane / positive regulation of endocytosis / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / immunoglobulin mediated immune response / maternal process involved in female pregnancy / complement activation, classical pathway / positive regulation of phagocytosis / carboxypeptidase activity / positive regulation of cardiac muscle contraction / antigen binding / multivesicular body / response to bacterium / negative regulation of smooth muscle cell proliferation / brush border membrane / virion component / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of immune response / antibacterial humoral response / virus receptor activity / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / apical plasma membrane / 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 / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / 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. ...Fibritin C-terminal / Fibritin C-terminal region / 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. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 / Trp-Asp (WD) repeats signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 2A / Spike glycoprotein / Fibritin / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse) / Enterobacteria phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsLau K / Ni D / Beckert B / Nazarov S / Myasnikov A / Pojer F / Stahlberg H / Uchikawa E
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR transcure Switzerland
Citation
Journal: PLoS Pathog / Year: 2023
Title: Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range.
Authors: Dongchun Ni / Priscilla Turelli / Bertrand Beckert / Sergey Nazarov / Emiko Uchikawa / Alexander Myasnikov / Florence Pojer / Didier Trono / Henning Stahlberg / Kelvin Lau /
Abstract: Investigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported ...Investigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported to be transmitted from humans to various animals after requiring relatively few mutations. There is significant interest in describing how the virus interacts with mice as they are well adapted to human environments, are used widely as infection models and can be infected. Structural and binding data of the mouse ACE2 receptor with the Spike protein of newly identified SARS-CoV-2 variants are needed to better understand the impact of immune system evading mutations present in variants of concern (VOC). Previous studies have developed mouse-adapted variants and identified residues critical for binding to heterologous ACE2 receptors. Here we report the cryo-EM structures of mouse ACE2 bound to trimeric Spike ectodomains of four different VOC: Beta, Omicron BA.1, Omicron BA.2.12.1 and Omicron BA.4/5. These variants represent the oldest to the newest variants known to bind the mouse ACE2 receptor. Our high-resolution structural data complemented with bio-layer interferometry (BLI) binding assays reveal a requirement for a combination of mutations in the Spike protein that enable binding to the mouse ACE2 receptor.
#1: Journal: Biorxiv / Year: 2023
Title: Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range
Authors: Ni D / Turelli P / Beckert B / Nazarov S / Uchikawa E / Myasnikov A / Pojer F / Trono D / Stahlberg H / Lau K
History
DepositionAug 13, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15591.png

Downloads & links

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Map

FileDownload / File: emd_15591.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationb2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 360 pix.
= 365.184 Å		1.01 Å/pix.
x 360 pix.
= 365.184 Å		1.01 Å/pix.
x 360 pix.
= 365.184 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.134
Minimum - Maximum-1.1156366 - 1.5602524
Average (Standard dev.)-0.00041178128 (±0.026490794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 365.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: b2

Fileemd_15591_additional_1.map
Annotationb2
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Half map: b2

Fileemd_15591_half_map_1.map
Annotationb2
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Histogram

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Half map: b2

Fileemd_15591_half_map_2.map
Annotationb2
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Sample components

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Entire : SARS-COV2 BA.2.12.1 bound to mouse ACE2

EntireName: SARS-COV2 BA.2.12.1 bound to mouse ACE2
Components
  • Complex: SARS-COV2 BA.2.12.1 bound to mouse ACE2
    • Complex: SARS-CoV-2 BA.2.12.1 spike protein
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: Mouse ACE2
      • Protein or peptide: Processed angiotensin-converting enzyme 2,Ig gamma-2A chain C region, membrane-bound form
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-COV2 BA.2.12.1 bound to mouse ACE2

SupramoleculeName: SARS-COV2 BA.2.12.1 bound to mouse ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 430 KDa

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Supramolecule #2: SARS-CoV-2 BA.2.12.1 spike protein

SupramoleculeName: SARS-CoV-2 BA.2.12.1 spike protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Mouse ACE2

SupramoleculeName: Mouse ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Processed angiotensin-converting enzyme 2,Ig gamma-2A chain C reg...

MacromoleculeName: Processed angiotensin-converting enzyme 2,Ig gamma-2A chain C region, membrane-bound form
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 101.892125 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTASLTEEN AKTFLNNFNQ EAEDLSYQSS LASWNYNTNI TEENAQKMSE AAAKWSAFY EEQSKTAQSF SLQEIQTPII KRQLQALQQS GSSALSADKN KQLNTILNTM STIYSTGKVC NPKNPQECLL L EPGLDEIM ...String:
MGTLSAPPCT QRIKWKGLLL TASLLNFWNL PTTASLTEEN AKTFLNNFNQ EAEDLSYQSS LASWNYNTNI TEENAQKMSE AAAKWSAFY EEQSKTAQSF SLQEIQTPII KRQLQALQQS GSSALSADKN KQLNTILNTM STIYSTGKVC NPKNPQECLL L EPGLDEIM ATSTDYNSRL WAWEGWRAEV GKQLRPLYEE YVVLKNEMAR ANNYNDYGDY WRGDYEAEGA DGYNYNRNQL IE DVERTFA EIKPLYEHLH AYVRRKLMDT YPSYISPTGC LPAHLLGDMW GRFWTNLYPL TVPFAQKPNI DVTDAMMNQG WDA ERIFQE AEKFFVSVGL PHMTQGFWAN SMLTEPADGR KVVCHPTAWD LGHGDFRIKM CTKVTMDNFL TAHHEMGHIQ YDMA YARQP FLLRNGANEG FHEAVGEIMS LSAATPKHLK SIGLLPSDFQ EDSETEINFL LKQALTIVGT LPFTYMLEKW RWMVF RGEI PKEQWMKKWW EMKREIVGVV EPLPHDETYC DPASLFHVSN DYSFIRYYTR TIYQFQFQEA LCQAAKYNGS LHKCDI SNS TEAGQKLLKM LSLGNSEPWT KALENVVGAR NMDVKPLLNY FQPLFDWLKE QNRNSFVGWN TEWSPYADTG LEVLFQG PM DEPRGPTIKP CPPCKCPAPN LLGGPSVFIF PPKIKDVLMI SLSPIVTCVV VDVSEDDPDV QISWFVNNVE VHTAQTQT H REDYNSTLRV VSALPIQHQD WMSGKEFKCK VNNKDLPAPI ERTISKPKGS VRAPQVYVLP PPEEEMTKKQ VTLTCMVTD FMPEDIYVEW TNNGKTELNY KNTEPVLDSD GSYFMYSKLR VEKKNWVERN SYSCSVVHEG LHNHHTTKSF SRTPGKHHHH HHHHHH

UniProtKB: Angiotensin-converting enzyme 2, Immunoglobulin heavy constant gamma 2A

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Macromolecule #2: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 142.428719 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV ...String:
MFVFLVLLPL VSSQCVNLIT RTQSYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLD VYYHKNNKSW MESEFRVYSS A NNCTFEYV SQPFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LGRDLPQGFS ALEPLVDLPI GINITRFQTL LA LHRSYLT PGDSSSGWTA GAAAYYVGYL QPRTFLLKYN ENGTITDAVD CALDPLSETK CTLKSFTVEK GIYQTSNFRV QPT ESIVRF PNITNLCPFD EVFNATRFAS VYAWNRKRIS NCVADYSVLY NFAPFFAFKC YGVSPTKLND LCFTNVYADS FVIR GNEVS QIAPGQTGNI ADYNYKLPDD FTGCVIAWNS NKLDSKVGGN YNYQYRLFRK SNLKPFERDI STEIYQAGNK PCNGV AGFN CYFPLRSYGF RPTYGVGHQP YRVVVLSFEL LHAPATVCGP KKSTNLVKNK CVNFNFNGLT GTGVLTESNK KFLPFQ QFG RDIADTTDAV RDPQTLEILD ITPCSFGGVS VITPGTNTSN QVAVLYQGVN CTEVPVAIHA DQLTPTWRVY STGSNVF QT RAGCLIGAEY VNNSYECDIP IGAGICASYQ TQTKSHGSAS SVASQSIIAY TMSLGAENSV AYSNNSIAIP TNFTISVT T EILPVSMTKT SVDCTMYICG DSTECSNLLL QYGSFCTQLK RALTGIAVEQ DKNTQEVFAQ VKQIYKTPPI KYFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGA ALQIPFAMQM AYRFNGIGVT QNVLYENQKL IANQFNSAIG KIQDSLSSTA SALGKLQDVV NHNAQALNTL V KQLSSKFG AISSVLNDIL SRLDPPEAEV QIDRLITGRL QSLQTYVTQQ LIRAAEIRAS ANLAATKMSE CVLGQSKRVD FC GKGYHLM SFPQSAPHGV VFLHVTYVPA QEKNFTTAPA ICHDGKAHFP REGVFVSNGT HWFVTQRNFY EPQIITTDNT FVS GNCDVV IGIVNNTVYD PLQPELDSFK EELDKYFKNH TSPDVDLGDI SGINASVVNI QKEIDRLNEV AKNLNESLID LQEL GKYEQ GSGYIPEAPR DGQAYVRKDG EWVLLSTFLG RSLEVLFQGP GHHHHHHHHS AWSHPQFEKG GGSGGGGSGG SAWSH PQFE K

UniProtKB: Spike glycoprotein, Fibritin

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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: 1 / 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: 7.5
VitrificationCryogen name: ETHANE
DetailsSARS-CoV-2 BA.2.12.1 bound to mouse ACE2

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80674
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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