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Yorodumi- PDB-7ytn: Crystal structure of SARS-CoV-2 Alpha RBD in complex with the D27... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ytn | ||||||
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Title | Crystal structure of SARS-CoV-2 Alpha RBD in complex with the D27LEY neutralizing antibody Fab fragment | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN/VIRAL PROTEIN / Antibody / Antigen / Complex / SARS-CoV-2 / RBD / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / 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: 3.51 Å | ||||||
Authors | Jeong, B.S. / Jeon, J.Y. / Oh, B.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Front Immunol / Year: 2022 Title: Structural basis for the broad and potent cross-reactivity of an N501Y-centric antibody against sarbecoviruses. Authors: Jeong, B.S. / Jeon, J.Y. / Lai, C.J. / Yun, H.Y. / Jung, J.U. / Oh, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ytn.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ytn.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 7ytn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ytn_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
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Full document | 7ytn_full_validation.pdf.gz | 447.2 KB | Display | |
Data in XML | 7ytn_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 7ytn_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/7ytn ftp://data.pdbj.org/pub/pdb/validation_reports/yt/7ytn | HTTPS FTP |
-Related structure data
Related structure data | 7vyrS 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
#1: Antibody | Mass: 25335.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 26249.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
#3: Protein | Mass: 29314.240 Da / Num. of mol.: 1 / Fragment: RBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.62 Å3/Da / Density % sol: 65.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 200 mM ammonium citrate tribasic (pH 7.0), 20% (v/v) polyethyleneglycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 19, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.51→38.99 Å / Num. obs: 15579 / % possible obs: 91.8 % / Redundancy: 21.6 % / Biso Wilson estimate: 34.96 Å2 / Rpim(I) all: 0.164 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.51→3.63 Å / Num. unique obs: 15500 / Rpim(I) all: 0.1265 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7vyr Resolution: 3.51→38.99 Å / SU ML: 0.3615 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.6502 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: 40.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.51→38.99 Å
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Refine LS restraints |
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LS refinement shell |
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