+Open data
-Basic information
Entry | Database: PDB / ID: 6isc | |||||||||
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Title | complex structure of mCD226-ecto and hCD155-D1 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / complex structure / mCD226 / CD155 / NK cell receptor | |||||||||
Function / homology | Function and homology information positive regulation of Fc receptor mediated stimulatory signaling pathway / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell cytokine production / positive regulation of mast cell activation / regulation of viral entry into host cell ...positive regulation of Fc receptor mediated stimulatory signaling pathway / susceptibility to T cell mediated cytotoxicity / coreceptor-mediated virion attachment to host cell / establishment of mitochondrion localization / susceptibility to natural killer cell mediated cytotoxicity / positive regulation of immunoglobulin mediated immune response / Nectin/Necl trans heterodimerization / positive regulation of natural killer cell cytokine production / positive regulation of mast cell activation / regulation of viral entry into host cell / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / acrosome assembly / positive regulation of natural killer cell mediated cytotoxicity / apical junction complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of T cell receptor signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / cell adhesion molecule binding / cytoskeleton organization / adherens junction / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / integrin binding / virus receptor activity / signaling receptor activity / cell adhesion / external side of plasma membrane / fusion of virus membrane with host plasma membrane / focal adhesion / protein kinase binding / cell surface / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Wang, H. / Qi, J. / Zhang, S. / Li, Y. / Tan, S. / Gao, G.F. | |||||||||
Funding support | China, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Binding mode of the side-by-side two-IgV molecule CD226/DNAM-1 to its ligand CD155/Necl-5. Authors: Wang, H. / Qi, J. / Zhang, S. / Li, Y. / Tan, S. / Gao, G.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6isc.cif.gz | 156.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6isc.ent.gz | 122.1 KB | Display | PDB format |
PDBx/mmJSON format | 6isc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6isc_validation.pdf.gz | 458.2 KB | Display | wwPDB validaton report |
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Full document | 6isc_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 6isc_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6isc_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6isc ftp://data.pdbj.org/pub/pdb/validation_reports/is/6isc | HTTPS FTP |
-Related structure data
Related structure data | 6isaSC 6isbC 3eow 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: 25370.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd226, Pta1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K4F0 |
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#2: Protein | Mass: 13095.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PVR, PVS / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P15151 |
#3: Sugar | ChemComp-NAG / |
#4: 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: 2.36 Å3/Da / Density % sol: 47.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris (pH 8.0), 0.15 M ammonium sulfate, and 15% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97923 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 18895 / % possible obs: 99.5 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.036 / Rsym value: 0.099 / Net I/σ(I): 23.456 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6 % / Num. unique obs: 1772 / CC1/2: 0.798 / Rpim(I) all: 0.378 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ISA, 3EOW Resolution: 2.2→42.273 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→42.273 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -7.359 Å / Origin y: -14.6221 Å / Origin z: 23.3973 Å
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Refinement TLS group | Selection details: all |