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Yorodumi- PDB-7nkt: RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nkt | ||||||
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Title | RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226 | ||||||
Components |
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Keywords | VIRAL PROTEIN / RBD / SARS-CoV2 / neutralizing nanobody / complex / NM1226 | ||||||
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 / 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 Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ostertag, E. / Zocher, G. / Stehle, T. | ||||||
Citation | Journal: Embo Rep. / Year: 2021 Title: NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies. Authors: Wagner, T.R. / Ostertag, E. / Kaiser, P.D. / Gramlich, M. / Ruetalo, N. / Junker, D. / Haering, J. / Traenkle, B. / Becker, M. / Dulovic, A. / Schweizer, H. / Nueske, S. / Scholz, A. / Zeck, ...Authors: Wagner, T.R. / Ostertag, E. / Kaiser, P.D. / Gramlich, M. / Ruetalo, N. / Junker, D. / Haering, J. / Traenkle, B. / Becker, M. / Dulovic, A. / Schweizer, H. / Nueske, S. / Scholz, A. / Zeck, A. / Schenke-Layland, K. / Nelde, A. / Strengert, M. / Walz, J.S. / Zocher, G. / Stehle, T. / Schindler, M. / Schneiderhan-Marra, N. / Rothbauer, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nkt.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nkt.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nkt_validation.pdf.gz | 474.4 KB | Display | wwPDB validaton report |
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Full document | 7nkt_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 7nkt_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 7nkt_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/7nkt ftp://data.pdbj.org/pub/pdb/validation_reports/nk/7nkt | HTTPS FTP |
-Related structure data
Related structure data | 7b27C 6xc4S 6z1zS C: citing same article (ref.) S: Starting model for refinement |
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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 AAABBB
#1: Protein | Mass: 25951.219 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 / Cell line (production host): Expi293F GnTI- / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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#2: Antibody | Mass: 15960.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) |
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 141 molecules
#4: Chemical | ChemComp-PO4 / | ||
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#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 50mM K2HPO4, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2020 |
Radiation | Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→46.103 Å / Num. obs: 28115 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.999 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.297→2.44 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4500 / CC1/2: 0.484 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z1Z, 6XC4 Resolution: 2.3→46.103 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.113 / SU ML: 0.145 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.168 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: 59.942 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→46.103 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 |
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