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Yorodumi- PDB-7l0n: Circulating SARS-CoV-2 spike N439K variants maintain fitness whil... -
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-Basic information
Entry | Database: PDB / ID: 7l0n | ||||||
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Title | Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity | ||||||
Components |
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Keywords | VIRAL PROTEIN/HYDROLASE / COVID-19 / SARS-CoV-2 / variant RBD / viral protein-receptor complex / VIRAL PROTEIN / VIRAL PROTEIN-HYDROLASE complex | ||||||
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 / negative regulation of signaling receptor activity / 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 / tryptophan transport / positive regulation of gap junction assembly / negative regulation of signaling receptor activity / 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 / 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 / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / virus receptor activity / regulation of inflammatory response / regulation of cell population proliferation / endopeptidase activity / Potential therapeutics for SARS / 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 / 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 / apical plasma membrane / symbiont entry into host cell / 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 / zinc ion binding / extracellular exosome / 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 / molecular replacement / Resolution: 2.78 Å | ||||||
Authors | Snell, G. / Czudnochowski, N. / Dillen, J. / Nix, J.C. / Croll, T.I. / Corti, D. | ||||||
Citation | Journal: Cell / Year: 2021 Title: Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Authors: Thomson, E.C. / Rosen, L.E. / Shepherd, J.G. / Spreafico, R. / da Silva Filipe, A. / Wojcechowskyj, J.A. / Davis, C. / Piccoli, L. / Pascall, D.J. / Dillen, J. / Lytras, S. / Czudnochowski, ...Authors: Thomson, E.C. / Rosen, L.E. / Shepherd, J.G. / Spreafico, R. / da Silva Filipe, A. / Wojcechowskyj, J.A. / Davis, C. / Piccoli, L. / Pascall, D.J. / Dillen, J. / Lytras, S. / Czudnochowski, N. / Shah, R. / Meury, M. / Jesudason, N. / De Marco, A. / Li, K. / Bassi, J. / O'Toole, A. / Pinto, D. / Colquhoun, R.M. / Culap, K. / Jackson, B. / Zatta, F. / Rambaut, A. / Jaconi, S. / Sreenu, V.B. / Nix, J. / Zhang, I. / Jarrett, R.F. / Glass, W.G. / Beltramello, M. / Nomikou, K. / Pizzuto, M. / Tong, L. / Cameroni, E. / Croll, T.I. / Johnson, N. / Di Iulio, J. / Wickenhagen, A. / Ceschi, A. / Harbison, A.M. / Mair, D. / Ferrari, P. / Smollett, K. / Sallusto, F. / Carmichael, S. / Garzoni, C. / Nichols, J. / Galli, M. / Hughes, J. / Riva, A. / Ho, A. / Schiuma, M. / Semple, M.G. / Openshaw, P.J.M. / Fadda, E. / Baillie, J.K. / Chodera, J.D. / Rihn, S.J. / Lycett, S.J. / Virgin, H.W. / Telenti, A. / Corti, D. / Robertson, D.L. / Snell, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l0n.cif.gz | 661.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l0n.ent.gz | 537.5 KB | Display | PDB format |
PDBx/mmJSON format | 7l0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7l0n_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7l0n_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7l0n_validation.xml.gz | 112 KB | Display | |
Data in CIF | 7l0n_validation.cif.gz | 151.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/7l0n ftp://data.pdbj.org/pub/pdb/validation_reports/l0/7l0n | HTTPS FTP |
-Related 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 EFRS
#5: Protein | Mass: 69153.664 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, angiotensin-converting enzyme 2 #6: Protein | Mass: 22963.859 Da / Num. of mol.: 2 / Fragment: 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 BDACLNHM
#1: Antibody | Mass: 23204.697 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23369.947 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 23729.389 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 3 types, 11 molecules
#7: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#8: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#15: Sugar | ChemComp-NAG / |
-Non-polymers , 8 types, 273 molecules
#9: Chemical | ChemComp-CL / #10: Chemical | #11: Chemical | ChemComp-NA / #12: Chemical | ChemComp-PG5 / | #13: Chemical | ChemComp-PG4 / | #14: Chemical | #16: Chemical | #17: 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: 3.76 Å3/Da / Density % sol: 67.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.09 M Buffer System 3 pH 8.5 contains Tris (base); BICINE 27% Precipitant Mix 2 contains Ethylene glycol and PEG8000 0.1 M Ammonium sulfate |
-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 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 31, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.78→48.95 Å / Num. obs: 131453 / % possible obs: 94.8 % / Redundancy: 7.2 % / CC1/2: 0.97 / Rmerge(I) obs: 0.506 / Rpim(I) all: 0.202 / Rrim(I) all: 0.545 / Net I/σ(I): 3.3 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6M0j, 7jx3 Resolution: 2.78→48.9 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.836 / SU B: 31.038 / SU ML: 0.539 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.067 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 194.15 Å2 / Biso mean: 86.099 Å2 / Biso min: 18.99 Å2
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Refinement step | Cycle: final / Resolution: 2.78→48.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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