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Yorodumi- PDB-1bqs: THE CRYSTAL STRUCTURE OF MUCOSAL ADDRESSIN CELL ADHESION MOLECULE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bqs | |||||||||
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Title | THE CRYSTAL STRUCTURE OF MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1) | |||||||||
Components | PROTEIN (MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1) | |||||||||
Keywords | MEMBRANE PROTEIN / CELL ADHESION PROTEIN / MADCAM-1 / IMMUNOGLOBULIN FOLD / I-SET FOLD / CELL ADHESION GLYCOPROTEIN / INTEGRIN RECOGINITION | |||||||||
Function / homology | Function and homology information positive regulation of lymphocyte migration / integrin binding involved in cell-matrix adhesion / leukocyte tethering or rolling / heterotypic cell-cell adhesion / positive regulation of leukocyte migration / receptor clustering / Integrin cell surface interactions / cell-matrix adhesion / integrin-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...positive regulation of lymphocyte migration / integrin binding involved in cell-matrix adhesion / leukocyte tethering or rolling / heterotypic cell-cell adhesion / positive regulation of leukocyte migration / receptor clustering / Integrin cell surface interactions / cell-matrix adhesion / integrin-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell adhesion / immune response / signal transduction / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.2 Å | |||||||||
Authors | Tan, K. / Casasnovas, J.M. / Liu, J.H. / Briskin, M.J. / Springer, T.A. / Wang, J.-H. | |||||||||
Citation | Journal: Structure / Year: 1998 Title: The structure of immunoglobulin superfamily domains 1 and 2 of MAdCAM-1 reveals novel features important for integrin recognition. Authors: Tan, K. / Casasnovas, J.M. / Liu, J.H. / Briskin, M.J. / Springer, T.A. / Wang, J.H. #1: Journal: J.Immunol. / Year: 1996 Title: Human Mucosal Addressin Cell Adhesion Molecule-1(Ma Demonstrates Structural and Functional Similarities Alpha4Beta7-Integrin Binding Domains of Murine Madc But Extreme Divergence of Mucin-Like Sequence Authors: Shyjan, A.M. / Bertagnolli, M. / Kenney, C.J. / Briskin, M.J. #2: Journal: Cell(Cambridge,Mass.) / Year: 1994 Title: Traffic Signals for Lymphocyte Recirculation and Le Emigration Authors: Springer, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bqs.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bqs.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/1bqs ftp://data.pdbj.org/pub/pdb/validation_reports/bq/1bqs | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22118.039 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR REGION WITH TWO IG-LIKE DOMAINS / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: HEMATOPOIETIC AND ENDOTHELIAL CELLS / Plasmid: PBJ5-GS-MADCAM-1 / References: UniProt: Q13477 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
Compound details | MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1) IS IMPORTANT IN LYMPHOCYTE HOMING TO MUCOSAL ...MUCOSAL ADDRESSIN CELL ADHESION MOLECULE-1 (MADCAM-1) IS IMPORTANT IN LYMPHOCYTE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 50 % | ||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop Details: PROTEIN SOLUTION:17 MG/ML. CRYSTALLIZATION SOLUTION: 10% PEG 400, 0.5M LI2SO4, PH 7.5-8.0., VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS PH range low: 8 / PH range high: 7.5 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 1997 / Details: DOUBLE FOCUSED MIRROR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. obs: 11229 / % possible obs: 92.2 % / Observed criterion σ(I): 3 / Redundancy: 7.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 6.4 / % possible all: 96.1 |
Reflection | *PLUS Num. measured all: 87803 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→15 Å / σ(F): 2
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Displacement parameters | Biso mean: 44.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 44.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.369 / % reflection Rfree: 10 % / Rfactor Rwork: 0.327 |