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- EMDB-32758: Cryo-EM structure of SARS-CoV-2 spike receptor-binding domain in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-32758
TitleCryo-EM structure of SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2
Map data
Sample
  • Complex: SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2
    • Complex: SARS-CoV-2 spike receptor-binding domain
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: sea lion ACE2
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscomplex / VIRAL PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / cilium / metallopeptidase 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 / proteolysis / extracellular space / identical protein binding / membrane / metal ion binding / 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, 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 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsLi S / Han P
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) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32758.png

Downloads & links

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Map

FileDownload / File: emd_32758.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: 0.35
Minimum - Maximum-1.8354124 - 2.6413827
Average (Standard dev.)-0.0004257334 (±0.061094902)
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-2 spike receptor-binding domain in complex with sea lion ACE2

EntireName: SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2
Components
  • Complex: SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2
    • Complex: SARS-CoV-2 spike receptor-binding domain
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: sea lion ACE2
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2

SupramoleculeName: SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mammalia (mammals)

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Supramolecule #2: SARS-CoV-2 spike receptor-binding domain

SupramoleculeName: SARS-CoV-2 spike receptor-binding domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: sea lion ACE2

SupramoleculeName: sea lion ACE2 / type: complex / 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: 93.009812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLGSSWLLLS LAALTAARST TEDLVKTFLE KFNSEAEELS YQSSLASWNY NTNITDENVQ KMNDAGAKWS AFYEEQSKQA KTYPLEEIQ DSTVKRQLQA LQHSGSSVLS ADKSQRLNTI LNAMSTIYST GKACNPNNPQ ECLLLEPGLD DIMANSRDYN E RLWAWEGW ...String:
MLGSSWLLLS LAALTAARST TEDLVKTFLE KFNSEAEELS YQSSLASWNY NTNITDENVQ KMNDAGAKWS AFYEEQSKQA KTYPLEEIQ DSTVKRQLQA LQHSGSSVLS ADKSQRLNTI LNAMSTIYST GKACNPNNPQ ECLLLEPGLD DIMANSRDYN E RLWAWEGW RSEVGKQLRP LYEEYVALKN EMARANNYED YGDYWRGDYE EEWTNGYNYS RDQLIKDVEQ TFTQIQPLYE HL HAYVRAK LMDTYPSHMS PTGCLPAHLL GDMWGRFWTN LYPLTVPFGQ KPNIDVTDTM VNQSWDARRI FEEAEKFFVS VGL PNMTQG FWENSMLTEP GDSRKVVCHP TAWDLGKHDF RIKMCTKVTM DDFLTAHHEM GHIQYDMAYA AQPFLLRNGA NEGF HEAVG EIMSLSAATP KHLKNIGLLP PGFSEDNETD INFLFKQALT IVGTLPFTYM LEKWRWMVFK GEIPKEQWMK KWWEM KRDL VGVVEPLPHD ETYCDPASLF HVANDYSFIR YYTRTIYQFQ FQEALCQIAK HEGPLHKCDI SNSSEAGQTL LQMLKL GRS KPWTLALYRV VGAKNMDVRP LLNYFDPLFT WLKEQNRNSF VGWNTDWSPY ADQSIKVRIS LKSALGEKAY EWNDNEM YL FRSSIAYAMR EYFSKVKNQM IPFVEDNVWV NNLKPRISFT FFVTSPGNMS DIIPRADVEE AIRMSRGRIN DAFRLDDN S LEFLGIQPTL EPPYQPPVTI WLIVFGVVMA VVVVGIVLLI FSGIRSRRKN DQATSEENPY ASVNLSKGEN NPGFQNVDD VQTSSF

UniProtKB: Angiotensin-converting enzyme

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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 2
Molecular weightTheoretical: 21.873496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCGP

UniProtKB: Spike glycoprotein

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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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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: 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182315
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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