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Yorodumi- EMDB-37006: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37006 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-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 / positive regulation of gap junction assembly / tryptophan transport / 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 / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / carboxypeptidase activity / positive regulation of cardiac muscle contraction / brush border membrane / cilium / metallopeptidase activity / virus receptor activity / endopeptidase 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 / symbiont-mediated suppression of host innate immune response / 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 / 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 / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mesocricetus auratus (golden hamster) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Niu S / Zhao ZN / Chai Y / Gao GF | |||||||||
Funding support | China, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37006.map.gz | 453.8 MB | EMDB map data format | |
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Header (meta data) | emd-37006-v30.xml emd-37006.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_37006.png | 35.8 KB | ||
Filedesc metadata | emd-37006.cif.gz | 6 KB | ||
Others | emd_37006_half_map_1.map.gz emd_37006_half_map_2.map.gz | 475.3 MB 475.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37006 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37006 | HTTPS FTP |
-Validation report
Summary document | emd_37006_validation.pdf.gz | 865.2 KB | Display | EMDB validaton report |
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Full document | emd_37006_full_validation.pdf.gz | 864.8 KB | Display | |
Data in XML | emd_37006_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | emd_37006_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37006 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37006 | HTTPS FTP |
-Related structure data
Related structure data | 8ka8MC 8kc2C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37006.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_37006_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37006_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden ...
Entire | Name: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement) |
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Components |
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-Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden ...
Supramolecule | Name: 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
Supramolecule | Name: Golden hamster angiotensin-converting enzyme 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Mesocricetus auratus (golden hamster) |
-Supramolecule #3: Delta RBD
Supramolecule | Name: Delta RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Macromolecule #1: Angiotensin-converting enzyme
Macromolecule | Name: Angiotensin-converting enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases) |
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Source (natural) | Organism: Mesocricetus auratus (golden hamster) |
Molecular weight | Theoretical: 68.943328 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 21.848492 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 141067 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |