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- EMDB-39229: Cryo-EM structure of SARS-CoV-2 alpha variant spike protein in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-39229
TitleCryo-EM structure of SARS-CoV-2 alpha variant spike protein in complex with raccoon dog ACE2 (local refinement)
Map data
Sample
  • Complex: SARS-CoV-2 alpha spike in complex with raccoon dog ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / alpha / RBD / raccoon dog / ACE2 / VIRAL PROTEIN-HYDROLASE Complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase 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 / 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. / 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 / 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
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Nyctereutes procyonoides (raccoon dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsLi LJ / Luo CL / Qi JX / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: PLoS Pathog / Year: 2024
Title: Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Authors: Chunliang Luo / Linjie Li / Yuhang Gu / Hangchuan Zhang / Zepeng Xu / Junqing Sun / Kaiyuan Shi / Sufang Ma / Wen-Xia Tian / Kefang Liu / George F Gao /
Abstract: Raccoon dog was proposed as a potential host of SARS-CoV-2, but no evidence support such a notion. In our study, we investigated the binding affinities of raccoon dog ACE2 (rdACE2) to the spike (S) ...Raccoon dog was proposed as a potential host of SARS-CoV-2, but no evidence support such a notion. In our study, we investigated the binding affinities of raccoon dog ACE2 (rdACE2) to the spike (S) protein receptor binding domain (RBD) of SARS-CoV-2 prototype (PT) and its variants. It revealed that the binding affinities of RBD from SARS-CoV-2 variants were generally lower than that of the PT RBD. Through structural and functional analyses, we found amino acids H34 and M82 play pivotal roles in maintaining the binding affinity of ACE2 to different SARS-CoV-2 sub-variants. These results suggest that raccoon dogs exhibit lower susceptibility to SARS-CoV-2 compared to those animal species with a high prevalence of SARS-CoV-2 transmission.
History
DepositionFeb 25, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateApr 30, 2025-
Current statusApr 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39229.png

Downloads & links

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Map

FileDownload / File: emd_39229.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 560 pix.
= 386.4 Å		0.69 Å/pix.
x 560 pix.
= 386.4 Å		0.69 Å/pix.
x 560 pix.
= 386.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.1380183 - 2.5734723
Average (Standard dev.)-0.0017403278 (±0.0100843515)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 386.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39229_msk_1.map
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Additional map: #1

Fileemd_39229_additional_1.map
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Half map: #2

Fileemd_39229_half_map_1.map
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Half map: #1

Fileemd_39229_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 alpha spike in complex with raccoon dog ACE2

EntireName: SARS-CoV-2 alpha spike in complex with raccoon dog ACE2
Components
  • Complex: SARS-CoV-2 alpha spike in complex with raccoon dog ACE2
    • Protein or peptide: Angiotensin-converting enzyme
    • 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 alpha spike in complex with raccoon dog ACE2

SupramoleculeName: SARS-CoV-2 alpha spike in complex with raccoon dog ACE2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 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: Nyctereutes procyonoides (raccoon dog)
Molecular weightTheoretical: 70.600086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSTEDLVNTF LEKFNYEAEE LSYQSSLASW NYNTNITDEN LQKMNNAGAK WSAFYEEQSK LAKTYPLEEI QDSTVKRQLR ALQHSGSSV LSADKNQRLN TILNSMSTIY STGKACNPSN PQECLLLEPG LDDIMENSKD YNERLWAWEG WRSEVGKQLR P LYEEYVAL ...String:
QSTEDLVNTF LEKFNYEAEE LSYQSSLASW NYNTNITDEN LQKMNNAGAK WSAFYEEQSK LAKTYPLEEI QDSTVKRQLR ALQHSGSSV LSADKNQRLN TILNSMSTIY STGKACNPSN PQECLLLEPG LDDIMENSKD YNERLWAWEG WRSEVGKQLR P LYEEYVAL KNEMARANNY EDYGDYWRGD YEEEWENGYN YSRNQLIDDV EHTFTQIMPL YQHLHAYVRT KLMDTYPSYI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTN AMVNQSWDAR KIFKEAEKFF VSVGLPNMTQ GFWENSMLTE PSD SWKVVC HPTAWDLGRG DFRIKMCTKV TMDDFLTAHH EMGHIQYDMA YAAQPFLLRN GANEGFHEAV GEIMSLSAAT PNHL KNIGL LPPSFFEDSE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGEIPKDQW MKTWWEMKRN IVGVVEPVPH DETYC DPAS LFHVANDYSF IRYYTRTIYQ FQFQEALCQI AKHEGPLHKC DISNSSEAGQ KLLEMLKLGK SKPWTYALEI VVGAKN MDV RPLLNYFEPL FTWLKEQNRN SFVGWNTDWS PYADQSHHHH HH

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 / Strain: Alpha
Molecular weightTheoretical: 25.171408 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF ...String:
RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSASFSTFK CYGVSPTKLN DLCFTNVYAD SFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCVIAWN SNNLDSKVGG NYNYLYRLFR KSNLKPFERD ISTEIYQAGS T PCNGVEGF NCYFPLQSYG FQPTYGVGYQ PYRVVVLSFE LLHAPATVCG PKKSTNLVKN KCVNF

UniProtKB: Spike glycoprotein

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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

MicroscopeTFS 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 306176
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: RANDOM ASSIGNMENT

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