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Yorodumi- PDB-1g1t: CRYSTAL STRUCTURE OF E-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH SLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g1t | |||||||||
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Title | CRYSTAL STRUCTURE OF E-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH SLEX | |||||||||
Components | E-SELECTIN | |||||||||
Keywords | IMMUNE SYSTEM / MEMBRANE PROTEIN / Lectin / EGF / Adhesion molecule / SLeX | |||||||||
Function / homology | Function and homology information actin filament-based process / sialic acid binding / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / leukocyte migration involved in inflammatory response / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cortical cytoskeleton ...actin filament-based process / sialic acid binding / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / leukocyte migration involved in inflammatory response / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cortical cytoskeleton / phospholipase binding / positive regulation of receptor internalization / activation of phospholipase C activity / response to tumor necrosis factor / clathrin-coated pit / response to interleukin-1 / response to cytokine / caveola / calcium-mediated signaling / Cell surface interactions at the vascular wall / transmembrane signaling receptor activity / regulation of inflammatory response / response to lipopolysaccharide / inflammatory response / membrane raft / external side of plasma membrane / perinuclear region of cytoplasm / extracellular space / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 1g1t.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g1t.ent.gz | 36 KB | Display | PDB format |
PDBx/mmJSON format | 1g1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/1g1t ftp://data.pdbj.org/pub/pdb/validation_reports/g1/1g1t | 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
#1: Protein | Mass: 18103.234 Da / Num. of mol.: 1 / Fragment: LECTIN/EGF DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary [CHO] cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16581 |
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#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)] ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, Tris-HCl, CaCl2, PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→15 Å / Num. all: 29493 / Num. obs: 29493 / % possible obs: 92.4 % / Observed criterion σ(I): 3 / Redundancy: 8.8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 47.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.22 / % possible all: 62 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 260283 |
Reflection shell | *PLUS % possible obs: 62 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→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: 1.5→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |