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- EMDB-15592: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local) -

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Basic information

Entry
Database: EMDB / ID: EMD-15592
TitleBA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local)
Map datab4m
Sample
  • Complex: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local)
    • Complex: SARS-CoV-2 BA.4/5 spike protein
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: Mouse ACE2Angiotensin-converting enzyme 2
      • Protein or peptide: Processed angiotensin-converting enzyme 2,Ig gamma-2A chain C region, A allele
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / positive regulation of amino acid transport / immunoglobulin receptor binding / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior ...Metabolism of Angiotensinogen to Angiotensins / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / positive regulation of amino acid transport / immunoglobulin receptor binding / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / metallocarboxypeptidase activity / complement activation, classical pathway / carboxypeptidase activity / positive regulation of cardiac muscle contraction / antigen binding / virion component / negative regulation of smooth muscle cell proliferation / brush border membrane / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / virus receptor activity / antibacterial humoral response / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / endopeptidase activity / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulin/major histocompatibility complex, conserved site ...Fibritin C-terminal / Fibritin C-terminal region / Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Trp-Asp (WD) repeats signature. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Ig gamma-2A chain C region, A allele / 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: 3.3 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 15, 2023-
Map releaseMar 15, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15592.png

Downloads & links

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Map

FileDownload / File: emd_15592.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationb4m
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.172
Minimum - Maximum-0.7450115 - 2.1135473
Average (Standard dev.)-0.0005953643 (±0.021475937)
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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Half map: b4m

Fileemd_15592_half_map_1.map
Annotationb4m
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: b4m

Fileemd_15592_half_map_2.map
Annotationb4m
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local)

EntireName: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local)
Components
  • Complex: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local)
    • Complex: SARS-CoV-2 BA.4/5 spike protein
      • Protein or peptide: Spike glycoprotein,Fibritin
    • Complex: Mouse ACE2Angiotensin-converting enzyme 2
      • Protein or peptide: Processed angiotensin-converting enzyme 2,Ig gamma-2A chain C region, A allele
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local)

SupramoleculeName: BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 430 KDa

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Supramolecule #2: SARS-CoV-2 BA.4/5 spike protein

SupramoleculeName: SARS-CoV-2 BA.4/5 spike protein / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Mouse ACE2

SupramoleculeName: Mouse ACE2 / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 142.143391 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
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 LDSKVGGNYN YRYRLFRKSN 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 SFIEDLLFNK VTLADAGFIK QYGDCLGDIA ARDLICAQKF NGLTVLPPLL TDEMIAQYTS ALLAGTITSG WTFGAGAAL QIPFAMQMAY RFNGIGVTQN VLYENQKLIA NQFNSAIGKI QDSLSSTASA 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 YEQGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGRS LEVLFQGPGH HHHHHHHSAW SHPQFEKGGG SGGGGSGGSA WSHPQ FEK

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

MacromoleculeName: Processed angiotensin-converting enzyme 2,Ig gamma-2A chain C region, A allele
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 101.733969 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 TEWSPYADLE VLFQGPM DE PRGPTIKPCP PCKCPAPNLL GGPSVFIFPP KIKDVLMISL SPIVTCVVVD VSEDDPDVQI SWFVNNVEVH TAQTQTHR E DYNSTLRVVS ALPIQHQDWM SGKEFKCKVN NKDLPAPIER TISKPKGSVR APQVYVLPPP EEEMTKKQVT LTCMVTDFM PEDIYVEWTN NGKTELNYKN TEPVLDSDGS YFMYSKLRVE KKNWVERNSY SCSVVHEGLH NHHTTKSFSR TPGKHHHHHH HHHH

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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 / N-Acetylglucosamine

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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
DetailsBA.4/5 SARS-CoV-2 Spike bound to mouse ACE2

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 58.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103496
FSC plot (resolution estimation)

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