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Yorodumi- PDB-7efr: Structure of SARS-CoV-2 spike receptor-binding domain in complex ... -
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-Basic information
Entry | Database: PDB / ID: 7efr | ||||||
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Title | Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (T27W,N330Y) | ||||||
Components |
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Keywords | VIRAL PROTEIN / receptor-binding domain / angiotensin converting enzyme 2 | ||||||
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 membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.494 Å | ||||||
Authors | Lu, G.W. / Ye, F. / Lin, X. | ||||||
Citation | Journal: Signal Transduct Target Ther / Year: 2021 Title: S19W, T27W, and N330Y mutations in ACE2 enhance SARS-CoV-2 S-RBD binding toward both wild-type and antibody-resistant viruses and its molecular basis. Authors: Ye, F. / Lin, X. / Chen, Z. / Yang, F. / Lin, S. / Yang, J. / Chen, H. / Sun, H. / Wang, L. / Wen, A. / Zhang, X. / Dai, Y. / Cao, Y. / Yang, J. / Shen, G. / Yang, L. / Li, J. / Wang, Z. / ...Authors: Ye, F. / Lin, X. / Chen, Z. / Yang, F. / Lin, S. / Yang, J. / Chen, H. / Sun, H. / Wang, L. / Wen, A. / Zhang, X. / Dai, Y. / Cao, Y. / Yang, J. / Shen, G. / Yang, L. / Li, J. / Wang, Z. / Wang, W. / Wei, X. / Lu, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7efr.cif.gz | 340.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7efr.ent.gz | 274.1 KB | Display | PDB format |
PDBx/mmJSON format | 7efr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7efr_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 7efr_full_validation.pdf.gz | 477 KB | Display | |
Data in XML | 7efr_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 7efr_validation.cif.gz | 43.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/7efr ftp://data.pdbj.org/pub/pdb/validation_reports/ef/7efr | HTTPS FTP |
-Related structure data
Related structure data | 7efpC 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: 69474.016 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 | ||||
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#2: Protein | Mass: 24402.463 Da / Num. of mol.: 1 / Fragment: UNP residues 321-537 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DTC2 | ||||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0 M Ammonium sulfate, 0.1 M Sodium HEPES pH7.5 , 2 % v/v PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 54217 / % possible obs: 100 % / Redundancy: 21 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.49→2.59 Å / Rmerge(I) obs: 1.173 / Num. unique obs: 5340 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LZG Resolution: 2.494→26.284 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
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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 max: 137.83 Å2 / Biso mean: 53.5594 Å2 / Biso min: 34.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.494→26.284 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 16.1108 Å / Origin y: 34.3238 Å / Origin z: 38.7118 Å
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Refinement TLS group |
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