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- PDB-7ekc: Structure of SARS-CoV-2 Gamma variant spike receptor-binding doma... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ekc | ||||||
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Title | Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed with human ACE2 | ||||||
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![]() | HYDROLASE/VIRAL PROTEIN / SARS-CoV-2 / spike / RBD / 501Y.V3 / ACE2 / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex | ||||||
Function / homology | ![]() 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 / Potential therapeutics for SARS / 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 / 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, P.C. / Su, C. / Zhang, Y.F. / Qi, J.X. / Gao, G.F. | ||||||
![]() | ![]() Title: Molecular insights into receptor binding of recent emerging SARS-CoV-2 variants. Authors: Han, P. / Su, C. / Zhang, Y. / Bai, C. / Zheng, A. / Qiao, C. / Wang, Q. / Niu, S. / Chen, Q. / Zhang, Y. / Li, W. / Liao, H. / Li, J. / Zhang, Z. / Cho, H. / Yang, M. / Rong, X. / Hu, Y. / ...Authors: Han, P. / Su, C. / Zhang, Y. / Bai, C. / Zheng, A. / Qiao, C. / Wang, Q. / Niu, S. / Chen, Q. / Zhang, Y. / Li, W. / Liao, H. / Li, J. / Zhang, Z. / Cho, H. / Yang, M. / Rong, X. / Hu, Y. / Huang, N. / Yan, J. / Wang, Q. / Zhao, X. / Gao, G.F. / Qi, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 380.6 KB | Display | ![]() |
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PDB format | ![]() | 274.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 39.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ekeC ![]() 7ekfC ![]() 7ekgC ![]() 7ekhC ![]() 6lzgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 69982.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases |
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#2: Protein | Mass: 25972.281 Da / Num. of mol.: 1 / Mutation: K417T, E484K, N501Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 51 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-ZN / |
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#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 12% w/v PEG 20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 31516 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 47.55 Å2 / CC1/2: 0.997 / Net I/σ(I): 17.884 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 29219 / CC1/2: 0.717 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6LZG Resolution: 2.8→19.92 Å / SU ML: 0.2674 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.592 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: 53.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.92 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 / Label seq-ID: 1
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