+Open data
-Basic information
Entry | Database: PDB / ID: 7e3j | ||||||
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Title | Crystal structure of SARS-CoV-2 RBD binding to dog ACE2 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / spike / RBD / receptor binding | ||||||
Function / homology | Function and homology information 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 ...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 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Canis lupus familiaris (dog) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Zhang, Z. / Zhang, Y. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: The molecular basis for SARS-CoV-2 binding to dog ACE2. Authors: Zhang, Z. / Zhang, Y. / Liu, K. / Li, Y. / Lu, Q. / Wang, Q. / Zhang, Y. / Wang, L. / Liao, H. / Zheng, A. / Ma, S. / Fan, Z. / Li, H. / Huang, W. / Bi, Y. / Zhao, X. / Wang, Q. / Gao, G.F. ...Authors: Zhang, Z. / Zhang, Y. / Liu, K. / Li, Y. / Lu, Q. / Wang, Q. / Zhang, Y. / Wang, L. / Liao, H. / Zheng, A. / Ma, S. / Fan, Z. / Li, H. / Huang, W. / Bi, Y. / Zhao, X. / Wang, Q. / Gao, G.F. / Xiao, H. / Tong, Z. / Qi, J. / Sun, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e3j.cif.gz | 414 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e3j.ent.gz | 297.6 KB | Display | PDB format |
PDBx/mmJSON format | 7e3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/7e3j ftp://data.pdbj.org/pub/pdb/validation_reports/e3/7e3j | HTTPS FTP |
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-Related structure data
Related structure data | 6lzgS S: Starting model for refinement |
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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: 84255.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 |
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#2: Protein | Mass: 21873.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P0DTC2 |
#3: Chemical | ChemComp-ZN / |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | Y |
Sequence details | The NCBI reference sequence for dog ACE2 is XP_025292925.2. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 2% 1,4-dioxane, 0.1 M tris pH 8.0,15% polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 8, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / Num. obs: 30355 / % possible obs: 98.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 56.13 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2989 / CC1/2: 0.819 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LZG Resolution: 2.99→48.26 Å / SU ML: 0.4216 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8093 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: 52.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.99→48.26 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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