+Open data
-Basic information
Entry | Database: PDB / ID: 6yz5 | |||||||||
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Title | H11-D4 complex with SARS-CoV-2 RBD | |||||||||
Components |
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Keywords | VIRAL PROTEIN / nanobody / complex / SARS-Cov-2 | |||||||||
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 / 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 Lama glama (llama) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Naismith, J.H. / Huo, J. / Mikolajek, H. / Ward, P. / Dumoux, M. / Owens, R.J. / Le Bas, A. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: H11-D4 complex with SARS-CoV-2 RBD Authors: Naismith, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yz5.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yz5.ent.gz | 118.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yz5_validation.pdf.gz | 477.9 KB | Display | wwPDB validaton report |
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Full document | 6yz5_full_validation.pdf.gz | 478.4 KB | Display | |
Data in XML | 6yz5_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 6yz5_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/6yz5 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/6yz5 | HTTPS FTP |
-Related structure data
Related structure data | 6zbpC 6ylaS 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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Unit cell |
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-Components
-Protein / Antibody / Sugars , 3 types, 3 molecules EF
#1: Protein | Mass: 23716.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Truncated version expressed Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2 |
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#2: Antibody | Mass: 15010.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) |
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 257 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / #6: 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: 2.9 Å3/Da / Density % sol: 57.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the ...Details: the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97623 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→46.41 Å / Num. obs: 40120 / % possible obs: 99 % / Redundancy: 19.7 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3066 / CC1/2: 0.7 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YLA Resolution: 1.8→46.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.394 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.096 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.22 Å2 / Biso mean: 35.176 Å2 / Biso min: 15.44 Å2
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Refinement step | Cycle: final / Resolution: 1.8→46.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / 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 |
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