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Yorodumi- PDB-7nl7: Crystal Structure of DC-SIGN in complex with a triazole-based gly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nl7 | ||||||
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Title | Crystal Structure of DC-SIGN in complex with a triazole-based glycomimetic ligand | ||||||
Components | DC-SIGN, CRD domain | ||||||
Keywords | SUGAR BINDING PROTEIN / lectin | ||||||
Function / homology | Function and homology information B cell adhesion / cell-cell recognition / peptide antigen transport / intracellular transport of virus / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation ...B cell adhesion / cell-cell recognition / peptide antigen transport / intracellular transport of virus / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation / host cell / D-mannose binding / antigen processing and presentation / positive regulation of T cell proliferation / CD209 (DC-SIGN) signaling / viral genome replication / endocytosis / peptide antigen binding / virus receptor activity / carbohydrate binding / adaptive immune response / intracellular signal transduction / immune response / symbiont entry into host cell / external side of plasma membrane / innate immune response / virion attachment to host cell / cell surface / extracellular region / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Jakob, R.P. / Cramer, J. / Lakkaichi, A. / Aliu, B. / Cattaneo, I. / Klein, S. / Jiang, X. / Rabbani, S. / Schwardt, O. / Ernst, B. / Maier, T. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2021 Title: Sweet Drugs for Bad Bugs: A Glycomimetic Strategy against the DC-SIGN-Mediated Dissemination of SARS-CoV-2. Authors: Cramer, J. / Lakkaichi, A. / Aliu, B. / Jakob, R.P. / Klein, S. / Cattaneo, I. / Jiang, X. / Rabbani, S. / Schwardt, O. / Zimmer, G. / Ciancaglini, M. / Abreu Mota, T. / Maier, T. / Ernst, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nl7.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nl7.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 7nl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/7nl7 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/7nl7 | HTTPS FTP |
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-Related structure data
Related structure data | 7nl6C 1sl4S 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: 18160.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD209, CLEC4L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NNX6 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-UH5 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M MgCl2, 0.1M Hepes 7.5, 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→51.39 Å / Num. obs: 9333 / % possible obs: 99.9 % / Redundancy: 19.5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.408 / Rpim(I) all: 0.094 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 20.2 % / Rmerge(I) obs: 2.35 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 906 / CC1/2: 0.745 / Rpim(I) all: 0.53 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SL4 Resolution: 2.1→51.39 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.16 / Stereochemistry target values: ML
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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 max: 122.77 Å2 / Biso mean: 36.7397 Å2 / Biso min: 18.78 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→51.39 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %
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