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Open data
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Basic information
Entry | Database: PDB / ID: 8oww | ||||||
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Title | B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan) | ||||||
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![]() | VIRAL PROTEIN / Nanobody / SARS-CoV-2 / receptor binding domain / complex | ||||||
Function / homology | ![]() 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 / 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cornish, K.A.S. / Naismith, J.H. / Owens, R.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Authors: Katy Cornish / Jiandong Huo / Luke Jones / Parul Sharma / Joseph W Thrush / Sahar Abdelkarim / Anja Kipar / Siva Ramadurai / Miriam Weckener / Halina Mikolajek / Sai Liu / Imogen Buckle / ...Authors: Katy Cornish / Jiandong Huo / Luke Jones / Parul Sharma / Joseph W Thrush / Sahar Abdelkarim / Anja Kipar / Siva Ramadurai / Miriam Weckener / Halina Mikolajek / Sai Liu / Imogen Buckle / Eleanor Bentley / Adam Kirby / Ximeng Han / Stephen M Laidlaw / Michelle Hill / Lauren Eyssen / Chelsea Norman / Audrey Le Bas / John Clarke / William James / James P Stewart / Miles Carroll / James H Naismith / Raymond J Owens / ![]() ![]() Abstract: The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. ...The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the 'arms race' with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328.9 KB | Display | ![]() |
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PDB format | ![]() | 207.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.7 KB | Display | ![]() |
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Full document | ![]() | 488.5 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8owtC ![]() 8owvC ![]() 8oytC ![]() 8oyuC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein / Antibody / Sugars , 3 types, 3 molecules AB![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 22644.416 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
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#2: Antibody | Mass: 13591.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 107 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-NO3 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Tris pH 8.5, PEG smear low Seeded from crystals grown in ammonium nitrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2022 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.969→45.079 Å / Num. obs: 25155 / % possible obs: 99.9 % / Redundancy: 53.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.203 / Net I/σ(I): 15.3 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.534 Å2
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Refinement step | Cycle: LAST / Resolution: 1.969→45.079 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection: ALL |