Entry | Database: PDB / ID: 7xwa |
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Title | Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2 |
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Components | - Processed angiotensin-converting enzyme 2
- Spike protein S1
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Keywords | VIRAL PROTEIN / Spike protein / Receptor / Coronavirus |
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Function / homology | Function and homology information
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 / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...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 / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / Maturation of spike protein / endopeptidase activity / 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 / Potential therapeutics for SARS / 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 entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / 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 / extracellular space / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membraneSimilarity search - Function Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / 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. ...Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature. / 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-terminalSimilarity search - Domain/homology |
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Biological species | Homo sapiens (human)
![](img/tx_virus.gif) Severe acute respiratory syndrome coronavirus 2 |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å |
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Authors | Suzuki, T. / Kimura, K. / Hashiguchi, T. |
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Funding support | Japan, 2items Organization | Grant number | Country |
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Ministry of Education, Culture, Sports, Science and Technology (Japan) | 20H05773 | Japan | Japan Science and Technology | JPMJCR20H8 | Japan |
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Citation | Journal: Cell / Year: 2022 Title: Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Authors: Kimura, I. / Yamasoba, D. / Tamura, T. / Nao, N. / Suzuki, T. / Oda, Y. / Mitoma, S. / Ito, J. / Nasser, H. / Zahradnik, J. / Uriu, K. / Fujita, S. / Kosugi, Y. / Wang, L. / Tsuda, M. / ...Authors: Kimura, I. / Yamasoba, D. / Tamura, T. / Nao, N. / Suzuki, T. / Oda, Y. / Mitoma, S. / Ito, J. / Nasser, H. / Zahradnik, J. / Uriu, K. / Fujita, S. / Kosugi, Y. / Wang, L. / Tsuda, M. / Kishimoto, M. / Ito, H. / Suzuki, R. / Shimizu, R. / Begum, M.M. / Yoshimatsu, K. / Kimura, K.T. / Sasaki, J. / Sasaki-Tabata, K. / Yamamoto, Y. / Nagamoto, T. / Kanamune, J. / Kobiyama, K. / Asakura, H. / Nagashima, M. / Sadamasu, K. / Yoshimura, K. / Shirakawa, K. / Takaori-Kondo, A. / Kuramochi, J. / Schreiber, G. / Ishii, K.J. / Hashiguchi, T. / Ikeda, T. / Saito, A. / Fukuhara, T. / Tanaka, S. / Matsuno, K. / Sato, K. |
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History | Deposition | May 26, 2022 | Deposition site: PDBJ / Processing site: PDBJ |
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Revision 1.0 | Sep 28, 2022 | Provider: repository / Type: Initial release |
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Revision 1.1 | Oct 19, 2022 | Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name |
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Revision 1.2 | Nov 2, 2022 | Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first |
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Revision 1.3 | Nov 29, 2023 | Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model |
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