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Yorodumi- PDB-7ekh: Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ekh | ||||||
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Title | Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2 | ||||||
Components |
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Keywords | HYDROLASE/VIRAL PROTEIN / SARS-CoV-2 / spike / RBD / Y453F / ACE2 / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex | ||||||
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 / negative regulation of signaling receptor activity / regulation of vasoconstriction ...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 / negative regulation of signaling receptor activity / 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 / Attachment and Entry / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of inflammatory response / regulation of cell population proliferation / endopeptidase activity / Potential therapeutics for SARS / 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 / Attachment and Entry / membrane fusion / 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 / symbiont entry into host cell / membrane raft / 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 membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Han, P.C. / Su, C. / Zhang, Y.F. / Qi, J.X. / Gao, G.F. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Authors: Han, P. / Su, C. / Zhang, Y. / Bai, C. / Zheng, A. / Qiao, C. / Wang, Q. / Niu, S. / Chen, Q. / Zhang, Y. / Li, W. / Liao, H. / Li, J. / Zhang, Z. / Cho, H. / Yang, M. / Rong, X. / Hu, Y. / ...Authors: Han, P. / Su, C. / Zhang, Y. / Bai, C. / Zheng, A. / Qiao, C. / Wang, Q. / Niu, S. / Chen, Q. / Zhang, Y. / Li, W. / Liao, H. / Li, J. / Zhang, Z. / Cho, H. / Yang, M. / Rong, X. / Hu, Y. / Huang, N. / Yan, J. / Wang, Q. / Zhao, X. / Gao, G.F. / Qi, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ekh.cif.gz | 381.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ekh.ent.gz | 273.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ekh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ekh_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7ekh_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7ekh_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 7ekh_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/7ekh ftp://data.pdbj.org/pub/pdb/validation_reports/ek/7ekh | HTTPS FTP |
-Related structure data
Related structure data | 7ekcC 7ekeC 7ekfC 7ekgC 6lzgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 69982.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases | ||||||
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#2: Protein | Mass: 25935.219 Da / Num. of mol.: 1 / Mutation: Y453F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 | ||||||
#3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES, pH 6.5, 10% w/v PEG 5000 MME, 12% v/v1-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 49236 / % possible obs: 99.8 % / Redundancy: 18.7 % / Biso Wilson estimate: 37.12 Å2 / CC1/2: 0.998 / Net I/σ(I): 19.826 |
Reflection shell | Resolution: 2.4→2.49 Å / Num. unique obs: 46716 / CC1/2: 0.565 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6lzg Resolution: 2.4→20.39 Å / SU ML: 0.2312 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2608 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20.39 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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