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Yorodumi- PDB-6o3o: Structure of human DNAM-1 (CD226) bound to nectin-like protein-5 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o3o | |||||||||
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Title | Structure of human DNAM-1 (CD226) bound to nectin-like protein-5 (necl-5) | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / immune receptor / immunoglobulin domain / adhesion molecule | |||||||||
Function / homology | Function and homology information cell recognition / 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 ...cell recognition / 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 / 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 / membrane raft / external side of plasma membrane / fusion of virus membrane with host plasma membrane / focal adhesion / protein kinase binding / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Deuss, F.A. / Watson, G.M. / Rossjohn, J. / Berry, R. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural basis for the recognition of nectin-like protein-5 by the human-activating immune receptor, DNAM-1. Authors: Deuss, F.A. / Watson, G.M. / Goodall, K.J. / Leece, I. / Chatterjee, S. / Fu, Z. / Thaysen-Andersen, M. / Andrews, D.M. / Rossjohn, J. / Berry, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o3o.cif.gz | 416 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o3o.ent.gz | 341.2 KB | Display | PDB format |
PDBx/mmJSON format | 6o3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o3o_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6o3o_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6o3o_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 6o3o_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o3/6o3o ftp://data.pdbj.org/pub/pdb/validation_reports/o3/6o3o | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 27690.170 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD226, DNAM1 / Production host: Homo sapiens (human) / References: UniProt: Q15762 #2: Protein | Mass: 34697.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PVR, PVS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15151 |
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-Sugars , 4 types, 16 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 106 molecules
#7: Chemical | #8: Water | ChemComp-HOH / | |
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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: 3.46 Å3/Da / Density % sol: 64.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 0.18M K2SO4, 10mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→105.5 Å / Num. obs: 42723 / % possible obs: 100 % / Redundancy: 19.7 % / Biso Wilson estimate: 69.71 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.094 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6171 / CC1/2: 0.642 / Rpim(I) all: 0.47 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R0N, 4FQP Resolution: 2.8→40.99 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.88 / SU R Cruickshank DPI: 0.501 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.482 / SU Rfree Blow DPI: 0.273 / SU Rfree Cruickshank DPI: 0.279
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Displacement parameters | Biso mean: 63.74 Å2
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Refine analyze | Luzzati coordinate error obs: 0.41 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→40.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.87 Å / Rfactor Rfree error: 0 / 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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