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- EMDB-32756: Cryo-EM structure of SARS-CoV spike receptor-binding domain in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-32756
TitleCryo-EM structure of SARS-CoV spike receptor-binding domain in complex with minke whale ACE2
Map data
Sample
  • Complex: SARS-CoV spike receptor-binding domain in complex with minke whale ACE2
    • Complex: minke whale ACE2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: SARS-CoV spike receptor-binding domain
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / Attachment and Entry / endocytosis involved in viral entry into host cell / cilium / SARS-CoV-1 activates/modulates innate immune responses ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / Attachment and Entry / endocytosis involved in viral entry into host cell / cilium / SARS-CoV-1 activates/modulates innate immune responses / metallopeptidase activity / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular space / identical protein binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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, N-terminal domain, SARS-CoV-like / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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, N-terminal domain, SARS-CoV-like / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesMammalia (mammals) / Severe acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsLi S / Han P / Qi J
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: Natl Sci Rev / Year: 2022
Title: Cross-species recognition and molecular basis of SARS-CoV-2 and SARS-CoV binding to ACE2s of marine animals.
Authors: Shihua Li / Ruirui Yang / Di Zhang / Pu Han / Zepeng Xu / Qian Chen / Runchu Zhao / Xin Zhao / Xiao Qu / Anqi Zheng / Liang Wang / Linjie Li / Yu Hu / Rong Zhang / Chao Su / Sheng Niu / ...Authors: Shihua Li / Ruirui Yang / Di Zhang / Pu Han / Zepeng Xu / Qian Chen / Runchu Zhao / Xin Zhao / Xiao Qu / Anqi Zheng / Liang Wang / Linjie Li / Yu Hu / Rong Zhang / Chao Su / Sheng Niu / Yanfang Zhang / Jianxun Qi / Kefang Liu / Qihui Wang / George F Gao /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has an extremely broad host range that includes hippopotami, which are phylogenetically closely related to whales. The cellular ACE2 ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has an extremely broad host range that includes hippopotami, which are phylogenetically closely related to whales. The cellular ACE2 receptor is one of the key determinants of the host range. Here, we found that ACE2s from several marine mammals and hippopotami could efficiently bind to the receptor-binding domain (RBD) of both SARS-CoV and SARS-CoV-2 and facilitate the transduction of SARS-CoV and SARS-CoV-2 pseudoviruses into ACE2-expressing cells. We further resolved the cryo-electron microscopy complex structures of the minke whale ACE2 and sea lion ACE2, respectively, bound to the RBDs, revealing that they have similar binding modes to human ACE2 when it comes to the SARS-CoV-2 RBD and SARS-CoV RBD. Our results indicate that marine mammals could potentially be new victims or virus carriers of SARS-CoV-2, which deserves further careful investigation and study. It will provide an early warning for the prospective monitoring of marine mammals.
History
DepositionJan 29, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateOct 19, 2022-
Current statusOct 19, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32756.png

Downloads & links

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Map

FileDownload / File: emd_32756.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.)
0.67 Å/pix.
x 360 pix.
= 240.84 Å		0.67 Å/pix.
x 360 pix.
= 240.84 Å		0.67 Å/pix.
x 360 pix.
= 240.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.669 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-1.5330484 - 2.222938
Average (Standard dev.)-0.0007171753 (±0.05300748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 240.84001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SARS-CoV spike receptor-binding domain in complex with minke whal...

EntireName: SARS-CoV spike receptor-binding domain in complex with minke whale ACE2
Components
  • Complex: SARS-CoV spike receptor-binding domain in complex with minke whale ACE2
    • Complex: minke whale ACE2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: SARS-CoV spike receptor-binding domain
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION

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Supramolecule #1: SARS-CoV spike receptor-binding domain in complex with minke whal...

SupramoleculeName: SARS-CoV spike receptor-binding domain in complex with minke whale ACE2
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mammalia (mammals)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #2: minke whale ACE2

SupramoleculeName: minke whale ACE2 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293

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Supramolecule #3: SARS-CoV spike receptor-binding domain

SupramoleculeName: SARS-CoV spike receptor-binding domain / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #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: Mammalia (mammals)
Molecular weightTheoretical: 85.789805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGSFWLLLS LVAVTAAQST TEEQAKTFLQ KFDHEAEDLS YRSSLASWNY NTNITDENVQ KMNAARAKWS AFYEEQSRIA KTYPLEEIQ NLTLKRQLQA LQQSGTSVLS ADKSKRLNTI LNTMSTIYSS GKVLDPNTQE YLVLEPGLDD IMENSEDYNR R LWAWEGWR ...String:
MSGSFWLLLS LVAVTAAQST TEEQAKTFLQ KFDHEAEDLS YRSSLASWNY NTNITDENVQ KMNAARAKWS AFYEEQSRIA KTYPLEEIQ NLTLKRQLQA LQQSGTSVLS ADKSKRLNTI LNTMSTIYSS GKVLDPNTQE YLVLEPGLDD IMENSEDYNR R LWAWEGWR AEVGKQLRPF YEEYVVLENE MARANNYEDY GDYWRGDYEV TGADGYDYSR NQLIADVERT FAEIKPLYEQ LH AYVRAKL MDAYPSRISP TGCLPAHLLG DMWGRFWTNL YPLTVPFGEK PSIDVTKEMQ NQSWDAKRIF KEAEKFFVSI GLP NMTQEF WVNSMLTEPG DGRKVVCHPT AWDLGKGDFR IKMCTKVTMD DFLTAHHEMG HIQYDMAYAT QPFLLRNGAN EGFH EAVGE IMSLSAATPH YLKALGLLPP DFYEDNVTEI NFLLKQALQI VGTLPFTYML EKWRWMVFKG EIPKEQWMQK WWEMK REIV GVVEPLPHDE TYCDPACLFH VAEDYSFIRY YTRTIYQFQF HEALCQTAKH EGPLYKCDIS NSTEAGQRLL QMLHLG KSE PWTLALENIV GVKTMDVKPL LNYFEPLLTW LKEQNRNSPV GWSTDWTPYS DQSIKVRISL KSALGEKAYE WNDNEMY LF QSSVAYAMRE YFSKVRNETI PFGEKDVWVS DLKPRISFNF FVTTPKNVSD IIPRTEVEEA IRMSRGRIND AFRLDDNS L EFLGIQPTLG PPYEPPVT

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Macromolecule #2: Spike protein S1

MacromoleculeName: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 21.624326 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NLCPFGEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPG QTGVIADYN YKLPDDFMGC VLAWNTRNID ATSTGNYNYK YRYLRHGKLR PFERDISNVP FSPDGKPCTP PALNCYWPLN D YGFYTTTG IGYQPYRVVV LSFEGSLEVL FQ

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146539
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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