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Yorodumi- PDB-7w6r: Structure of Bat coronavirus RaTG13 spike receptor-binding domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w6r | ||||||
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Title | Structure of Bat coronavirus RaTG13 spike receptor-binding domain complexed with its receptor equine ACE2 | ||||||
Components |
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Keywords | VIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / endocytosis involved in viral entry into host cell / cilium / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / endocytosis involved in viral entry into host cell / cilium / metallopeptidase activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / proteolysis / extracellular space / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Equus caballus (horse) Bat coronavirus RaTG13 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Xu, Z.P. / Liu, K.F. / Han, P. / Qi, J.X. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses Authors: Xu, Z. / Kang, X. / Han, P. / Du, P. / Li, L. / Zheng, A. / Deng, C. / Qi, J. / Zhao, X. / Wang, Q. / Liu, K. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7w6r.cif.gz | 396.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7w6r.ent.gz | 266.6 KB | Display | PDB format |
PDBx/mmJSON format | 7w6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/7w6r ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w6r | HTTPS FTP |
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-Related structure data
Related structure data | 7w6uC 6lzgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 69777.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: ACE2 / Production host: Escherichia coli (E. coli) References: UniProt: F6V9L3, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Protein | Mass: 25150.430 Da / Num. of mol.: 1 / Fragment: RBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bat coronavirus RaTG13 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A6B9WHD3 |
#3: Chemical | ChemComp-ZN / |
#4: Sugar | ChemComp-NAG / |
#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: 2.95 Å3/Da / Density % sol: 58.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Lithium chloride, 0.1M Tris 8.0, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 32977 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 42.55 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.075 / Rrim(I) all: 0.187 / Rsym value: 0.171 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3285 / CC1/2: 0.793 / Rpim(I) all: 0.448 / Rsym value: 1.032 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LZG Resolution: 2.6→46.16 Å / SU ML: 0.2429 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7803 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: 43.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→46.16 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 | Refine-ID: X-RAY DIFFRACTION
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