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Yorodumi- PDB-2edo: Solution structure of the first ig-like domain from human CD48 antigen -
+Open data
-Basic information
Entry | Database: PDB / ID: 2edo | ||||||
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Title | Solution structure of the first ig-like domain from human CD48 antigen | ||||||
Components | CD48 antigenCD48 | ||||||
Keywords | CELL ADHESION / beta-sandwich / ig-fold / B-lymphocyte activation marker BLAST-1 / BCM1 surface antigen / Leukocyte antigen MEM-102 / TCT.1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information : / regulation of adaptive immune response / : / leukocyte migration / antigen binding / Cell surface interactions at the vascular wall / defense response / signaling receptor activity / membrane raft / extracellular exosome ...: / regulation of adaptive immune response / : / leukocyte migration / antigen binding / Cell surface interactions at the vascular wall / defense response / signaling receptor activity / membrane raft / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Nagashima, K. / Nagashima, T. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first ig-like domain from human CD48 antigen Authors: Nagashima, K. / Nagashima, T. / Yoshida, M. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2edo.cif.gz | 768.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2edo.ent.gz | 646.2 KB | Display | PDB format |
PDBx/mmJSON format | 2edo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/2edo ftp://data.pdbj.org/pub/pdb/validation_reports/ed/2edo | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13901.872 Da / Num. of mol.: 1 / Fragment: V-set Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: CD48, BCM1, BLAST1 / Plasmid: P060411-11 / References: UniProt: P09326 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: spectrometer_id 1 for 3D_13C-separated_NOESY; spectrometer_id 2 for 3D_15N-separated_NOESY |
-Sample preparation
Details | Contents: 1.15mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl 1mM d-DTT; 0.02% NaN3, 10% D2O; 90% H2O Solvent system: 10% D2O; 90% H2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |