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Yorodumi- PDB-7wue: Crystal structure of SARS-CoV-2 Receptor Binding Domain in comple... -
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-Basic information
Entry | Database: PDB / ID: 7wue | ||||||
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Title | Crystal structure of SARS-CoV-2 Receptor Binding Domain in complex with the monoclonal antibody m31A7 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / Spike / receptor binding domain / m31A7 / monoclonal antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM 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 / membrane fusion / 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 / 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 | Severe acute respiratory syndrome coronavirus 2 Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Mohapatra, A. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: Vaccination with SARS-CoV-2 spike protein lacking glycan shields elicits enhanced protective responses in animal models. Authors: Han-Yi Huang / Hsin-Yu Liao / Xiaorui Chen / Szu-Wen Wang / Cheng-Wei Cheng / Md Shahed-Al-Mahmud / Yo-Min Liu / Arpita Mohapatra / Ting-Hua Chen / Jennifer M Lo / Yi-Min Wu / Hsiu-Hua Ma / ...Authors: Han-Yi Huang / Hsin-Yu Liao / Xiaorui Chen / Szu-Wen Wang / Cheng-Wei Cheng / Md Shahed-Al-Mahmud / Yo-Min Liu / Arpita Mohapatra / Ting-Hua Chen / Jennifer M Lo / Yi-Min Wu / Hsiu-Hua Ma / Yi-Hsuan Chang / Ho-Yang Tsai / Yu-Chi Chou / Yi-Ping Hsueh / Ching-Yen Tsai / Pau-Yi Huang / Sui-Yuan Chang / Tai-Ling Chao / Han-Chieh Kao / Ya-Min Tsai / Yen-Hui Chen / Chung-Yi Wu / Jia-Tsrong Jan / Ting-Jen Rachel Cheng / Kuo-I Lin / Che Ma / Chi-Huey Wong / Abstract: A major challenge to end the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to develop a broadly protective vaccine that elicits long-term immunity. As the key ...A major challenge to end the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is to develop a broadly protective vaccine that elicits long-term immunity. As the key immunogen, the viral surface spike (S) protein is frequently mutated, and conserved epitopes are shielded by glycans. Here, we revealed that S protein glycosylation has site-differential effects on viral infectivity. We found that S protein generated by lung epithelial cells has glycoforms associated with increased infectivity. Compared to the fully glycosylated S protein, immunization of S protein with N-glycans trimmed to the mono-GlcNAc-decorated state (S) elicited stronger immune responses and better protection for human angiotensin-converting enzyme 2 (hACE2) transgenic mice against variants of concern (VOCs). In addition, a broadly neutralizing monoclonal antibody was identified from S-immunized mice that could neutralize wild-type SARS-CoV-2 and VOCs with subpicomolar potency. Together, these results demonstrate that removal of glycan shields to better expose the conserved sequences has the potential to be an effective and simple approach for developing a broadly protective SARS-CoV-2 vaccine. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wue.cif.gz | 260.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wue.ent.gz | 207.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wue_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7wue_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7wue_validation.xml.gz | 48 KB | Display | |
Data in CIF | 7wue_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/7wue ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wue | HTTPS FTP |
-Related structure data
Related structure data | 7wuhC 7c01S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 21873.496 Da / Num. of mol.: 2 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 #2: Antibody | Mass: 25621.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #3: Antibody | Mass: 26564.006 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | Source method: isolated from a genetically manipulated source Has ligand of interest | Y | |
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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: 3.35 Å3/Da / Density % sol: 63.26 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2.0 M Ammonia sulfate, 0.1M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 8, 2021 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→48.91 Å / Num. obs: 33348 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 66.59 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.11 / Rrim(I) all: 0.214 / Net I/σ(I): 5.7 / Num. measured all: 114117 / Scaling rejects: 125 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7C01 Resolution: 3.2→47.61 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.62 / Stereochemistry target values: ML
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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 max: 142.24 Å2 / Biso mean: 64.7867 Å2 / Biso min: 25.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→47.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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