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Yorodumi- PDB-7b27: RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b27 | ||||||
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Title | RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV2 / receptor binding domain / complex structure / neutralizing nanobody | ||||||
Function / homology | Function and homology information : / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Vicugna pacos (alpaca) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.902 Å | ||||||
Authors | Ostertag, E. / Zocher, G. / Stehle, T. | ||||||
Funding support | Germany, 1items
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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 | 7b27.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b27.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7b27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b27_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 7b27_full_validation.pdf.gz | 470.1 KB | Display | |
Data in XML | 7b27_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 7b27_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/7b27 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/7b27 | HTTPS FTP |
-Related structure data
Related structure data | 7nktC 6xc4S 6z1zS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24975.162 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Homo sapiens (human) / Strain (production host): Expi293F(TM) / References: UniProt: A0A6M6B9J6 #2: Antibody | Mass: 15463.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) #3: Sugar | 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: 2.55 Å3/Da / Density % sol: 51.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 200 mM MgCl2, 20% (w/v) PEG 3350, pH 5.9 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999998 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→46.5 Å / Num. obs: 18493 / % possible obs: 93.5 % / Redundancy: 6.06 % / Biso Wilson estimate: 61 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.207 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.9→2.98 Å / Mean I/σ(I) obs: 1.15 / Num. unique obs: 1340 / CC1/2: 0.662 / Rrim(I) all: 1.86 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6XC4, 6Z1Z Resolution: 2.902→30.002 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.88 / SU B: 30.768 / SU ML: 0.514 / Cross valid method: FREE R-VALUE / ESU R Free: 0.493 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: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.189 Å2
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Refinement step | Cycle: LAST / Resolution: 2.902→30.002 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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