+Open data
-Basic information
Entry | Database: PDB / ID: 5gni | ||||||
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Title | The crystal structure of PECAM-1 IgL1-2 trans-homophilic dimer | ||||||
Components | Platelet endothelial cell adhesion molecule | ||||||
Keywords | CELL ADHESION / Cell adhesion molecule / Immunoglobulin-like domain / Trans-homophilic dimer | ||||||
Function / homology | Function and homology information positive regulation of protein localization to cell-cell junction / diapedesis / cell recognition / glomerular endothelium development / monocyte extravasation / neutrophil extravasation / platelet alpha granule membrane / cell-cell adhesion via plasma-membrane adhesion molecules / bicellular tight junction assembly / negative regulation of immune response ...positive regulation of protein localization to cell-cell junction / diapedesis / cell recognition / glomerular endothelium development / monocyte extravasation / neutrophil extravasation / platelet alpha granule membrane / cell-cell adhesion via plasma-membrane adhesion molecules / bicellular tight junction assembly / negative regulation of immune response / establishment of endothelial barrier / leukocyte cell-cell adhesion / maintenance of blood-brain barrier / Platelet sensitization by LDL / homophilic cell adhesion via plasma membrane adhesion molecules / PECAM1 interactions / Integrin cell surface interactions / phagocytosis / secretory granule membrane / Cell surface interactions at the vascular wall / cell-cell adhesion / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / Platelet degranulation / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / membrane raft / positive regulation of protein phosphorylation / external side of plasma membrane / Neutrophil degranulation / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.008 Å | ||||||
Authors | Hu, M. / Zhang, H. / Liu, Q. / Hao, Q. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural Basis for Human PECAM-1-Mediated Trans-homophilic Cell Adhesion Authors: Hu, M. / Zhang, H. / Liu, Q. / Hao, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gni.cif.gz | 167.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gni.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gni.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/5gni ftp://data.pdbj.org/pub/pdb/validation_reports/gn/5gni | 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: 24549.855 Da / Num. of mol.: 2 / Fragment: UNP residues 28-232 / Mutation: N52Q, N84Q, N151Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PECAM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P16284 |
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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: 3.7 Å3/Da / Density % sol: 66.8 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH6.5, 1.8M (NH4)2SO4, 0.01M CoCl2 / PH range: 6.2-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0719 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0719 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 14823 / % possible obs: 99.7 % / Redundancy: 7.9 % / Rsym value: 0.086 / Net I/σ(I): 25.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.008→45.447 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.008→45.447 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 21.5017 Å / Origin y: 35.2888 Å / Origin z: 35.3553 Å
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Refinement TLS group | Selection details: all |