+Open data
-Basic information
Entry | Database: PDB / ID: 7fau | ||||||
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Title | Structure Determination of the NB1B11-RBD Complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / SARS-CoV-2 / RBD / Nanobody | ||||||
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 Camelidae (mammal) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Shi, Z.Z. / Li, X.X. / Wang, L. / Sun, Z.C. / Zhang, H.W. / Chen, X.C. / Cui, Q.Q. / Qiao, H.R. / Lan, Z.Y. / Zhang, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Structure / Year: 2022 Title: Structural basis of nanobodies neutralizing SARS-CoV-2 variants. Authors: Shi, Z. / Li, X. / Wang, L. / Sun, Z. / Zhang, H. / Chen, X. / Cui, Q. / Qiao, H. / Lan, Z. / Zhang, X. / Li, X. / Li, L. / Xu, J. / Gong, R. / Fan, C. / Geng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fau.cif.gz | 303.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fau.ent.gz | 204.6 KB | Display | PDB format |
PDBx/mmJSON format | 7fau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fau_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 7fau_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 7fau_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 7fau_validation.cif.gz | 37.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/7fau ftp://data.pdbj.org/pub/pdb/validation_reports/fa/7fau | HTTPS FTP |
-Related structure data
Related structure data | 7ch5S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 24649.645 Da / Num. of mol.: 2 / Fragment: Receptor-binding domain (RBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2 #2: Antibody | Mass: 13216.743 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | 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: 3.49 Å3/Da / Density % sol: 68.97 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350 and 0.1 M Zinc acetate, dehydrate |
-Data collection
Diffraction | Mean temperature: 97.15 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 64558 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 37.17 Å2 / CC1/2: 0.999 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.08→2.13 Å / Num. unique obs: 44904 / CC1/2: 0.578 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CH5 Resolution: 2.08→47.53 Å / SU ML: 0.2327 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1452 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: 40.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→47.53 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 40.0380681681 Å / Origin y: 43.911322398 Å / Origin z: 63.1233867048 Å
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Refinement TLS group | Selection details: all |