+Open data
-Basic information
Entry | Database: PDB / ID: 1k9i | |||||||||
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Title | Complex of DC-SIGN and GlcNAc2Man3 | |||||||||
Components | mDC-SIGN1B type I isoform | |||||||||
Keywords | SUGAR BINDING PROTEIN / C-type lectin / protein carbohydrate complex | |||||||||
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 / host cell / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion ...B cell adhesion / cell-cell recognition / peptide antigen transport / intracellular transport of virus / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / host cell / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation / 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: 2.5 Å | |||||||||
Authors | Feinberg, H. / Mitchell, D.A. / Drickamer, K. / Weis, W.I. | |||||||||
Citation | Journal: Science / Year: 2001 Title: Structural basis for selective recognition of oligosaccharides by DC-SIGN and DC-SIGNR. Authors: Feinberg, H. / Mitchell, D.A. / Drickamer, K. / Weis, W.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k9i.cif.gz | 284.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k9i.ent.gz | 232.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9i ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17817.660 Da / Num. of mol.: 10 / Fragment: Carbohydrate recognition domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 15281089, UniProt: Q9NNX6*PLUS #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Sequence details | This alanine residue was inserted after the initiator methionine residue at the N-terminus to ...This alanine residue was inserted after the initiator methionine residue at the N-terminus to ensure that the methionine would be efficiently removed. This strategy ensures that the polypeptide has a free N-terminus, allowing Edman degradation to confirm the identity and integrity of the bacterially expressed protein. | |
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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: 2.51 Å3/Da / Density % sol: 50.93 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG 8000, 0.1M Na-cacodilate, 200mM Ca Ac2. Protein solution containing 5mM CaCl2 and 5 mM oligosaccharide (Dextra M592)., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9646 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9646 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 60699 / Num. obs: 59357 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.053 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.266 / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 250720 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 99.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2477698.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.154 Å2 / ksol: 0.320351 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→26.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 6.1 % / Rfactor obs: 0.214 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 49.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.328 / % reflection Rfree: 7.2 % / Rfactor Rwork: 0.291 |