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Yorodumi- PDB-7tn0: SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tn0 | ||||||
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Title | SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab and S309 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / neutralizing monoclonal antibody / SARS-CoV-2 receptor human ACE2 / VIRAL PROTEIN-IMMUNE SYSTEM complex / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
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 / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...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 / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / 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 / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / 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 / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / 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) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | McCallum, M. / Czudnochowski, N. / Nix, J.C. / Croll, T.I. / SSGCID / Dillen, J.R. / Snell, G. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | 1items
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Citation | Journal: Science / Year: 2022 Title: Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement. Authors: Matthew McCallum / Nadine Czudnochowski / Laura E Rosen / Samantha K Zepeda / John E Bowen / Alexandra C Walls / Kevin Hauser / Anshu Joshi / Cameron Stewart / Josh R Dillen / Abigail E ...Authors: Matthew McCallum / Nadine Czudnochowski / Laura E Rosen / Samantha K Zepeda / John E Bowen / Alexandra C Walls / Kevin Hauser / Anshu Joshi / Cameron Stewart / Josh R Dillen / Abigail E Powell / Tristan I Croll / Jay Nix / Herbert W Virgin / Davide Corti / Gyorgy Snell / David Veesler / Abstract: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to ...The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and x-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tn0.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tn0.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 7tn0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tn0_validation.pdf.gz | 553 KB | Display | wwPDB validaton report |
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Full document | 7tn0_full_validation.pdf.gz | 571.8 KB | Display | |
Data in XML | 7tn0_validation.xml.gz | 106.8 KB | Display | |
Data in CIF | 7tn0_validation.cif.gz | 146.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/7tn0 ftp://data.pdbj.org/pub/pdb/validation_reports/tn/7tn0 | HTTPS FTP |
-Related structure data
Related structure data | 7tlyC 7tlzC 7tm0C 7jx3S C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules EFIS
#3: Protein | Mass: 69620.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9BYF1 #6: Protein | Mass: 24735.871 Da / Num. of mol.: 2 / Fragment: Receptor-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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-Antibody , 4 types, 8 molecules ADBCGNHM
#1: Antibody | Mass: 23204.697 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human) #2: Antibody | Mass: 24573.471 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human) #4: Antibody | Mass: 23369.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human) #5: Antibody | Mass: 23729.389 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 suspension / Production host: Homo sapiens (human) |
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-Sugars , 1 types, 11 molecules
#10: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 221 molecules
#7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-CL / #9: Chemical | #11: Water | ChemComp-HOH / | |
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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: 3.82 Å3/Da / Density % sol: 67.79 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 20% v/v Ethylene glycol, 10% w/v PEG 8000, 0.1 M Tris (base)/BICINE pH 8.5, 0.1 M NDSB-256 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07216 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Dec 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07216 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→48.91 Å / Num. obs: 121127 / % possible obs: 96.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 53.45 Å2 / CC1/2: 0.975 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.85→2.9 Å / Num. unique obs: 6212 / CC1/2: 0.209 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JX3 Resolution: 2.85→48.91 Å / SU ML: 0.4499 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9166 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: 63.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→48.91 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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