+Open data
-Basic information
Entry | Database: PDB / ID: 6zbp | ||||||
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Title | H11-H4 complex with SARS-CoV-2 | ||||||
Components |
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Keywords | ANTIVIRAL PROTEIN / Complex / llama / nanobody / antibody / 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 / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Naismith, J.H. / Huo, J. / Mikolajek, H. / Ward, P. / Dumoux, M. / Owens, R.J. / LeBas, A. | ||||||
Funding support | United Kingdom, 1items
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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 | 6zbp.cif.gz | 246.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zbp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/6zbp ftp://data.pdbj.org/pub/pdb/validation_reports/zb/6zbp | HTTPS FTP |
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-Related structure data
Related structure data | 6yz5SC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23716.580 Da / Num. of mol.: 1 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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#2: Antibody | Mass: 15045.752 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 / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium ...Details: Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of 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 N2 / 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: 1.85→57.151 Å / Num. obs: 35506 / % possible obs: 99.5 % / Redundancy: 19.7 % / CC1/2: 1 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.028 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 20.9 % / Rmerge(I) obs: 2.05 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2585 / CC1/2: 0.7 / Rpim(I) all: 0.46 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YZ5 Resolution: 1.85→57.151 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.218 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.116 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: 1.3 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.736 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→57.151 Å
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Refine LS restraints |
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LS refinement shell |
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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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