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Yorodumi- PDB-5xo2: Crystal structure of human paired immunoglobulin-like type 2 rece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xo2 | |||||||||
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Title | Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide II | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / membrane protein / immune receptor / viral entry inhibitor / glycopeptide | |||||||||
Function / homology | Function and homology information host cell Golgi membrane / MHC class I protein binding / host cell endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / signal transduction ...host cell Golgi membrane / MHC class I protein binding / host cell endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / signal transduction / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Human herpesvirus 1 (Herpes simplex virus type 1) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å | |||||||||
Authors | Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. ...Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / Anada, M. / Ose, T. / Hashimoto, S. / Maenaka, K. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structural and thermodynamic analyses reveal critical features of glycopeptide recognition by the human PILR alpha immune cell receptor. Authors: Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / ...Authors: Furukawa, A. / Kakita, K. / Yamada, T. / Ishizuka, M. / Sakamoto, J. / Hatori, N. / Maeda, N. / Ohsaka, F. / Saitoh, T. / Nomura, T. / Kuroki, K. / Nambu, H. / Arase, H. / Matsunaga, S. / Anada, M. / Ose, T. / Hashimoto, S. / Maenaka, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xo2.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xo2.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xo2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xo2_validation.pdf.gz | 975.3 KB | Display | wwPDB validaton report |
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Full document | 5xo2_full_validation.pdf.gz | 980.8 KB | Display | |
Data in XML | 5xo2_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 5xo2_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/5xo2 ftp://data.pdbj.org/pub/pdb/validation_reports/xo/5xo2 | HTTPS FTP |
-Related structure data
Related structure data | 5xofC 3wv0S 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: 13967.697 Da / Num. of mol.: 2 / Fragment: UNP residues 32-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PILRA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKJ1 #2: Protein/peptide | Mass: 609.671 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Human herpesvirus 1 (Herpes simplex virus type 1) References: UniProt: P06437 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: 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: 2.28 Å3/Da / Density % sol: 46.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M MES monohydrate pH 6.5, 1.6M Magnesium sulfate heptahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 13393 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8.4 / Num. unique all: 668 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WV0 Resolution: 2.201→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.201→50 Å
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LS refinement shell | Resolution: 2.201→2.279 Å /
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