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Yorodumi- PDB-6lzg: Structure of novel coronavirus spike receptor-binding domain comp... -
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Basic information
| Entry | Database: PDB / ID: 6lzg | |||||||||
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| Title | Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Novel Coronavirus / Spike protein / receptor | |||||||||
| Function / homology | Function and homology informationpositive 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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy ...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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human)![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Wang, Q.H. / Song, H. / Qi, J.X. | |||||||||
Citation | Journal: Cell / Year: 2020Title: Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Authors: Wang, Q. / Zhang, Y. / Wu, L. / Niu, S. / Song, C. / Zhang, Z. / Lu, G. / Qiao, C. / Hu, Y. / Yuen, K.Y. / Wang, Q. / Zhou, H. / Yan, J. / Qi, J. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6lzg.cif.gz | 387.2 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6lzg.ent.gz | 276.2 KB | Display | PDB format |
| PDBx/mmJSON format | 6lzg.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6lzg_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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| Full document | 6lzg_full_validation.pdf.gz | 1.8 MB | Display | |
| Data in XML | 6lzg_validation.xml.gz | 32.2 KB | Display | |
| Data in CIF | 6lzg_validation.cif.gz | 45.8 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/6lzg ftp://data.pdbj.org/pub/pdb/validation_reports/lz/6lzg | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2ajfS S: Starting model for refinement |
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| Similar structure data |
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
| #1: Protein | Mass: 69038.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases | ||||||||
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| #2: Protein | Mass: 23513.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: S, 2 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P0DTC2 | ||||||||
| #3: Sugar | ChemComp-NAG / #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.67 % |
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| Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES pH 6.5,10%w/v PEG 5000 MME,12% v/v 1-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: 0.97919 Å |
| Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 11, 2020 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
| Reflection | Resolution: 2.5→50 Å / Num. obs: 44981 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 21.6 % / Biso Wilson estimate: 35.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Net I/σ(I): 26.7 |
| Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 22.3 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4384 / CC1/2: 0.867 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 2ajf Resolution: 2.5→34.5 Å / SU ML: 0.2505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6451 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: 44.01 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.5→34.5 Å
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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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Homo sapiens (human)
X-RAY DIFFRACTION
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