+Open data
-Basic information
Entry | Database: PDB / ID: 1g1s | |||||||||
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Title | P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / MEMBRANE PROTEIN / selectin / lectin / egf / sulphated / slex | |||||||||
Function / homology | Function and homology information regulation of integrin activation / leukocyte adhesive activation / fucose binding / platelet dense granule membrane / glycosphingolipid binding / sialic acid binding / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / uropod / platelet alpha granule membrane ...regulation of integrin activation / leukocyte adhesive activation / fucose binding / platelet dense granule membrane / glycosphingolipid binding / sialic acid binding / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / uropod / platelet alpha granule membrane / leukocyte tethering or rolling / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / positive regulation of platelet activation / cellular response to interleukin-6 / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / leukocyte migration / plasma membrane => GO:0005886 / plasma membrane raft / hemopoiesis / : / response to cytokine / Cell surface interactions at the vascular wall / lipopolysaccharide binding / calcium-dependent protein binding / Platelet degranulation / virus receptor activity / heparin binding / defense response to Gram-negative bacterium / response to lipopolysaccharide / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / inflammatory response / external side of plasma membrane / signaling receptor binding / calcium ion binding / extracellular space / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å | |||||||||
Authors | Somers, W.S. / Camphausen, R.T. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLe(X) and PSGL-1. Authors: Somers, W.S. / Tang, J. / Shaw, G.D. / Camphausen, R.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g1s.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g1s.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 1g1s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/1g1s ftp://data.pdbj.org/pub/pdb/validation_reports/g1/1g1s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD
#1: Protein | Mass: 19131.238 Da / Num. of mol.: 2 / Fragment: LECTIN/EGF DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16109 #2: Protein/peptide | Mass: 3666.835 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q14242 #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 235 molecules
#4: Chemical | #5: Chemical | ChemComp-MRD / ( #6: Chemical | #7: 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: 3.15 Å3/Da / Density % sol: 60.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES, 10 mM TRIS, 150 mN NaCl, 4 mM CaCl2, 50 mM SrCl2, 5% PEG 6000, 33% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.99987 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1997 |
Radiation | Monochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→15 Å / Num. all: 44923 / Num. obs: 44923 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 4.63 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.7 / % possible all: 96.6 |
Reflection | *PLUS Num. measured all: 207998 |
Reflection shell | *PLUS % possible obs: 96.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: P-selectin Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.01 |