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Yorodumi- PDB-4hcr: Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hcr | ||||||
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Title | Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin superfamily / rolling and firm adhesion / integrin alpha4beta7 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Springer, T. / Yu, Y. / Zhu, J. | ||||||
Citation | Journal: TO BE PUBLISHED Title: A Different Fold with an Integrin-Binding Loop Specialized for Flexibility in Mucosal Addressin Cell Adhesion Molecule-1 Authors: Springer, T. / Yu, Y. / Zhu, J. / Wang, J.-H. / Huang, P.-S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hcr.cif.gz | 468.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hcr.ent.gz | 398.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/4hcr ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hcr | HTTPS FTP |
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-Related 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: Antibody | Mass: 24484.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 24166.002 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein | Mass: 22348.314 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MADCAM1 / Cell line (production host): HEK 293 GNTI(-) / Organ (production host): KIDNEY / Production host: Homo sapiens (human) / References: UniProt: Q13477 #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: 2.49 Å3/Da / Density % sol: 50.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Citrate pH 6.0, 18% (w/v) PEG 3350, 12% (w/v) myo-inositol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 1, 2011 |
Radiation | Monochromator: double silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48 Å / Num. all: 59513 / Num. obs: 59513 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.66 Å / σ(F): 1.99 / Phase error: 23.27 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0 Å / VDW probe radii: 0.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.66 Å
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Refine LS restraints |
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LS refinement shell |
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