+Open data
-Basic information
Entry | Database: PDB / ID: 7dhx | ||||||
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Title | Crystal structure of SARS-CoV-2 RBD binding to pangolin ACE2 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / envelope protein / complex | ||||||
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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 | Manis javanica (Malayan pangolin) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wang, Q.H. / Qi, J.X. / Wu, L.L. | ||||||
Funding support | China, 1items
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Citation | Journal: Chin.Sci.Bull. / Year: 2021 Title: Molecular basis of pangolin ACE2 engaged by COVID-19 virus Authors: Wu, L. / Gao, G. / Yan, J. / Wang, Q. / Niu, S. / Chen, Q. / Qi, J. / Zhang, Y. / Jiaqi, S. / Shi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dhx.cif.gz | 374.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dhx.ent.gz | 267 KB | Display | PDB format |
PDBx/mmJSON format | 7dhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/7dhx ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dhx | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 69944.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manis javanica (Malayan pangolin) / Production host: Spodoptera frugiperda (fall armyworm) | ||||||||
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#2: Protein | Mass: 23513.389 Da / Num. of mol.: 1 / Fragment: Receptor binding domain (RBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2 | ||||||||
#3: Sugar | #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | Sequence of ACE2 protein has been deposited to Genbank with accession ID XP_017505752.1. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.05M potassium phosphate, 20% w/v Polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 23, 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: 2.3→50 Å / Num. obs: 41945 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 30.41 Å2 / CC1/2: 0.824 / Net I/σ(I): 51.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 39596 / CC1/2: 0.832 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LZG Resolution: 2.3→33.93 Å / SU ML: 0.2833 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.028 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: 37.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.93 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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