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- EMDB-37006: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden ... -

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Entry
Database: EMDB / ID: EMD-37006
TitleCryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement)
Map data
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement)
    • Complex: Golden hamster angiotensin-converting enzyme 2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: Delta RBD
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Delta / spike protein / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / peptidyl-dipeptidase activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane ...Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / tryptophan transport / positive regulation of gap junction assembly / regulation of cardiac conduction / peptidyl-dipeptidase activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / cilium / metallopeptidase activity / virus receptor activity / 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 / 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 / membrane / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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 ...Collectrin domain / Renal amino acid transporter / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / 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
Similarity search - Domain/homology
Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesMesocricetus auratus (golden hamster) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsNiu S / Zhao ZN / Chai Y / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: J Virol / Year: 2024
Title: Structural basis and analysis of hamster ACE2 binding to different SARS-CoV-2 spike RBDs.
Authors: Sheng Niu / Zhennan Zhao / Zhimin Liu / Xiaoyu Rong / Yan Chai / Bin Bai / Pengcheng Han / Guijun Shang / Jianle Ren / Ying Wang / Xin Zhao / Kefang Liu / Wen-Xia Tian / Qihui Wang / George Fu Gao /
Abstract: Pet golden hamsters were first identified being infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant of concern (VOC) and transmitted the virus back to humans ...Pet golden hamsters were first identified being infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta variant of concern (VOC) and transmitted the virus back to humans in Hong Kong in January 2022. Here, we studied the binding of two hamster (golden hamster and Chinese hamster) angiotensin-converting enzyme 2 (ACE2) proteins to the spike protein receptor-binding domains (RBDs) of SARS-CoV-2 prototype and eight variants, including alpha, beta, gamma, delta, and four omicron sub-variants (BA.1, BA.2, BA.3, and BA.4/BA.5). We found that the two hamster ACE2s present slightly lower affinity for the RBDs of all nine SARS-CoV-2 viruses tested than human ACE2 (hACE2). Furthermore, the similar infectivity to host cells expressing hamster ACE2s and hACE2 was confirmed with the nine pseudotyped SARS-CoV-2 viruses. Additionally, we determined two cryo-electron microscopy (EM) complex structures of golden hamster ACE2 (ghACE2)/delta RBD and ghACE2/omicron BA.3 RBD. The residues Q34 and N82, which exist in many rodent ACE2s, are responsible for the lower binding affinity of ghACE2 compared to hACE2. These findings suggest that all SARS-CoV-2 VOCs may infect hamsters, highlighting the necessity of further surveillance of SARS-CoV-2 in these animals.IMPORTANCESARS-CoV-2 can infect many domestic animals, including hamsters. There is an urgent need to understand the binding mechanism of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants to hamster receptors. Herein, we showed that two hamster angiotensin-converting enzyme 2s (ACE2s) (golden hamster ACE2 and Chinese hamster ACE2) can bind to the spike protein receptor-binding domains (RBDs) of SARS-CoV-2 prototype and eight variants and that pseudotyped SARS-CoV-2 viruses can infect hamster ACE2-expressing cells. The binding pattern of golden hamster ACE2 to SARS-CoV-2 RBDs is similar to that of Chinese hamster ACE2. The two hamster ACE2s present slightly lower affinity for the RBDs of all nine SARS-CoV-2 viruses tested than human ACE2. We solved the cryo-electron microscopy (EM) structures of golden hamster ACE2 in complex with delta RBD and omicron BA.3 RBD and found that residues Q34 and N82 are responsible for the lower binding affinity of ghACE2 compared to hACE2. Our work provides valuable information for understanding the cross-species transmission mechanism of SARS-CoV-2.
History
DepositionAug 2, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37006.png

Downloads & links

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Map

FileDownload / File: emd_37006.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.066
Minimum - Maximum-0.0017328805 - 1.7312074
Average (Standard dev.)0.00029035052 (±0.0110342195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 450.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37006_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37006_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden ...

EntireName: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement)
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement)
    • Complex: Golden hamster angiotensin-converting enzyme 2
      • Protein or peptide: Angiotensin-converting enzyme
    • Complex: Delta RBD
      • Protein or peptide: Spike protein S1
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden ...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Golden hamster angiotensin-converting enzyme 2

SupramoleculeName: Golden hamster angiotensin-converting enzyme 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mesocricetus auratus (golden hamster)

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Supramolecule #3: Delta RBD

SupramoleculeName: Delta RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #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: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 68.943328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SIIEEQAKTF LDKFNQEAED LSYQSALASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK LAKNYSLQEV QNLTIKRQLQ ALQQSGSSA LSADKNKQLN TILNTMSTIY STGKVCNPKN PQECLLLEPG LDDIMATSTD YNERLWAWEG WRAEVGKQLR P LYEEYVVL ...String:
SIIEEQAKTF LDKFNQEAED LSYQSALASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK LAKNYSLQEV QNLTIKRQLQ ALQQSGSSA LSADKNKQLN TILNTMSTIY STGKVCNPKN PQECLLLEPG LDDIMATSTD YNERLWAWEG WRAEVGKQLR P LYEEYVVL KNEMARANNY EDYGDYWRGD YEAEGADGYN YNGNQLIEDV ERTFKEIKPL YEQLHAYVRT KLMNTYPSYI SP TGCLPAH LLGDMWGRFW TNLYPLTVPF GQKPNIDVTD AMVNQGWNAE RIFKEAEKFF VSVGLPYMTQ GFWENSMLTD PGD DRKVVC HPTAWDLGKG DFRIKMCTKV TMDNFLTAHH EMGHIQYDMA YATQPFLLRN GANEGFHEAV GEIMSLSAAT PEHL KSIGL LPSDFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FKGDIPKEQW MEKWWEMKRE IVGVVEPLPH DETYC DPAA LFHVSNDYSF IRYYTRTIYQ FQFQEALCQA AKHDGPLHKC DISNSTEAGQ KLLNMLRLGK SEPWTLALEN VVGARN MDV RPLLNYFEPL SVWLKEQNKN SFVGWNTDWS PYA

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: 21.848492 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY RYRLFRKSNL KPFERDISTE IYQAGSKPCN GVEGFNCYFP L QSYGFQPT ...String:
TNLCPFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTGKIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY RYRLFRKSNL KPFERDISTE IYQAGSKPCN GVEGFNCYFP L QSYGFQPT NGVGYQPYRV VVLSFELLHA PATVCG

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: 2 / 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: 8
VitrificationCryogen name: ETHANE

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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: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141067

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