+Open data
-Basic information
Entry | Database: PDB / ID: 8asy | |||||||||
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Title | SARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2 | |||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS CoV-2 / Omicron / BA.2.75 / ACE2 / complex / spike / RBD | |||||||||
Function / homology | Function and homology information 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 / cilium / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / 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 / 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 / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / membrane raft / 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 / extracellular exosome / zinc ion binding / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Zhou, D. / Huo, J. / Ren, J. / Stuart, D.I. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Cell Rep / Year: 2022 Title: A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75. Authors: Huo, J. / Dijokaite-Guraliuc, A. / Liu, C. / Zhou, D. / Ginn, H.M. / Das, R. / Supasa, P. / Selvaraj, M. / Nutalai, R. / Tuekprakhon, A. / Duyvesteyn, H.M.E. / Mentzer, A.J. / Skelly, D. / ...Authors: Huo, J. / Dijokaite-Guraliuc, A. / Liu, C. / Zhou, D. / Ginn, H.M. / Das, R. / Supasa, P. / Selvaraj, M. / Nutalai, R. / Tuekprakhon, A. / Duyvesteyn, H.M.E. / Mentzer, A.J. / Skelly, D. / Ritter, T.G. / Amini, A. / Bibi, S. / Adele, S. / Johnson, S.A. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Plowright, M. / Newman, T.A.H. / Hornsby, H. / de Silva, T.I. / Temperton, N. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Pollard, A.J. / Lambe, T. / Goulder, P. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8asy.cif.gz | 408.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8asy.ent.gz | 278 KB | Display | PDB format |
PDBx/mmJSON format | 8asy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/8asy ftp://data.pdbj.org/pub/pdb/validation_reports/as/8asy | HTTPS FTP |
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-Related structure data
Related structure data | 7zf7S S: Starting model for refinement |
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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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 70139.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1 |
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#2: Protein | Mass: 25154.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
-Sugars , 1 types, 6 molecules
#4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 14 molecules
#3: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-PGE / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1% (w/v) n-Octyl-b-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→76.2 Å / Num. obs: 29749 / % possible obs: 99.8 % / Redundancy: 26.8 % / Biso Wilson estimate: 58 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.443 / Rpim(I) all: 0.086 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.85→2.9 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1411 / CC1/2: 0.279 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ZF7 Resolution: 2.85→76.18 Å / SU ML: 0.4938 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1755 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 86.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→76.18 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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