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Yorodumi- EMDB-34217: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34217 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with rat ACE2 (local refinement) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-CoV-2 / Omicron BA.2 / spike protein / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex | |||||||||
Function / homology | Function and homology information Metabolism of Angiotensinogen to Angiotensins / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction ...Metabolism of Angiotensinogen to Angiotensins / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / brush border membrane / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / 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 / symbiont entry into host cell / 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 / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Zhao ZN / Xie YF / Chai Y / Qi JX / Gao GF | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants. Authors: Zhennan Zhao / Yufeng Xie / Bin Bai / Chunliang Luo / Jingya Zhou / Weiwei Li / Yumin Meng / Linjie Li / Dedong Li / Xiaomei Li / Xiaoxiong Li / Xiaoyun Wang / Junqing Sun / Zepeng Xu / ...Authors: Zhennan Zhao / Yufeng Xie / Bin Bai / Chunliang Luo / Jingya Zhou / Weiwei Li / Yumin Meng / Linjie Li / Dedong Li / Xiaomei Li / Xiaoxiong Li / Xiaoyun Wang / Junqing Sun / Zepeng Xu / Yeping Sun / Wei Zhang / Zheng Fan / Xin Zhao / Linhuan Wu / Juncai Ma / Odel Y Li / Guijun Shang / Yan Chai / Kefang Liu / Peiyi Wang / George F Gao / Jianxun Qi / Abstract: Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly ...Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34217.map.gz | 454.7 MB | EMDB map data format | |
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Header (meta data) | emd-34217-v30.xml emd-34217.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_34217.png | 34 KB | ||
Others | emd_34217_half_map_1.map.gz emd_34217_half_map_2.map.gz | 475.6 MB 475.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34217 | HTTPS FTP |
-Validation report
Summary document | emd_34217_validation.pdf.gz | 943.9 KB | Display | EMDB validaton report |
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Full document | emd_34217_full_validation.pdf.gz | 943.5 KB | Display | |
Data in XML | emd_34217_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_34217_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34217 | HTTPS FTP |
-Related structure data
Related structure data | 8gryMC 7yhwC 7yj3C 7yv8C 7yvuC 8h06C 8h5cC 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_34217.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_34217_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34217_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 Omicron BA.2 RBD in complex with ...
Entire | Name: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement) |
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Components |
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-Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with ...
Supramolecule | Name: Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
-Supramolecule #2: Rat angiotensin-converting enzyme 2
Supramolecule | Name: Rat angiotensin-converting enzyme 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #3: Omicron BA.2 RBD
Supramolecule | Name: Omicron BA.2 RBD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Processed angiotensin-converting enzyme 2
Macromolecule | Name: Processed angiotensin-converting enzyme 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 69.197625 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SLIEEKAESF LNKFNQEAED LSYQSSLASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK IAQNFSLQEI QNATIKRQLK ALQQSGSSA LSPDKNKQLN TILNTMSTIY STGKVCNSMN PQECFLLEPG LDEIMATSTD YNRRLWAWEG WRAEVGKQLR P LYEEYVVL ...String: SLIEEKAESF LNKFNQEAED LSYQSSLASW NYNTNITEEN AQKMNEAAAK WSAFYEEQSK IAQNFSLQEI QNATIKRQLK ALQQSGSSA LSPDKNKQLN TILNTMSTIY STGKVCNSMN PQECFLLEPG LDEIMATSTD YNRRLWAWEG WRAEVGKQLR P LYEEYVVL KNEMARANNY EDYGDYWRGD YEAEGVEGYN YNRNQLIEDV ENTFKEIKPL YEQLHAYVRT KLMEVYPSYI SP TGCLPAH LLGDMWGRFW TNLYPLTTPF LQKPNIDVTD AMVNQSWDAE RIFKEAEKFF VSVGLPQMTP GFWTNSMLTE PGD DRKVVC HPTAWDLGHG DFRIKMCTKV TMDNFLTAHH EMGHIQYDMA YAKQPFLLRN GANEGFHEAV GEIMSLSAAT PKHL KSIGL LPSNFQEDNE TEINFLLKQA LTIVGTLPFT YMLEKWRWMV FQDKIPREQW TKKWWEMKRE IVGVVEPLPH DETYC DPAS LFHVSNDYSF IRYYTRTIYQ FQFQEALCQA AKHDGPLHKC DISNSTEAGQ KLLNMLSLGN SGPWTLALEN VVGSRN MDV KPLLNYFQPL FVWLKEQNRN STVGWSTDWS PYAD UniProtKB: Angiotensin-converting enzyme 2 |
-Macromolecule #2: Spike protein S1
Macromolecule | Name: Spike protein S1 / type: protein_or_peptide / ID: 2 / Details: Omicron BA.2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 22.039873 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TNLCPFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNFA PFFAFKCYGV SPTKLNDLCF TNVYADSFVI RGNEVSQIAP GQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP L RSYGFRPT ...String: TNLCPFDEVF NATRFASVYA WNRKRISNCV ADYSVLYNFA PFFAFKCYGV SPTKLNDLCF TNVYADSFVI RGNEVSQIAP GQTGNIADY NYKLPDDFTG CVIAWNSNKL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGNKPCN GVAGFNCYFP L RSYGFRPT YGVGHQPYRV VVLSFELLHA PATVCGP UniProtKB: Spike glycoprotein |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 1 / 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: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50491 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |