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Yorodumi- PDB-2wng: complete extracellular structure of human signal regulatory prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wng | ||||||
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Title | complete extracellular structure of human signal regulatory protein (SIRP) alpha | ||||||
Components | TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1 | ||||||
Keywords | CELL ADHESION / SIGNAL REGULATORY PROTEIN ALPHA / IMMUNOGLOBULIN SUPERFAMILY / PHOSPHOPROTEIN / DISULFIDE BOND / PAIRED RECEPTOR / ALTERNATIVE SPLICING / IMMUNOGLOBULIN DOMAIN / SIRP / CD47 / SIRPA / MEMBRANE / SH3-BINDING / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / GTPase regulator activity / cell-cell adhesion mediator activity ...negative regulation of I-kappaB phosphorylation / cellular response to interleukin-12 / monocyte extravasation / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / protein binding involved in heterotypic cell-cell adhesion / regulation of interleukin-1 beta production / regulation of type II interferon production / GTPase regulator activity / cell-cell adhesion mediator activity / protein antigen binding / negative regulation of nitric oxide biosynthetic process / negative regulation of interferon-beta production / negative regulation of JNK cascade / regulation of tumor necrosis factor production / regulation of nitric oxide biosynthetic process / negative regulation of phagocytosis / regulation of interleukin-6 production / Signal regulatory protein family interactions / negative regulation of interleukin-6 production / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of tumor necrosis factor production / negative regulation of cytokine production involved in inflammatory response / cellular response to interleukin-1 / positive regulation of phagocytosis / protein tyrosine kinase binding / negative regulation of protein phosphorylation / Cell surface interactions at the vascular wall / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / SH3 domain binding / cellular response to type II interferon / cellular response to hydrogen peroxide / cell migration / positive regulation of T cell activation / regulation of gene expression / protein phosphatase binding / cellular response to lipopolysaccharide / cell adhesion / Neutrophil degranulation / cell surface / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Hatherley, D. / Graham, S.C. / Harlos, K. / Stuart, D.I. / Barclay, A.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structure of Signal-Regulatory Protein Alpha: A Link to Antigen Receptor Evolution. Authors: Hatherley, D. / Graham, S.C. / Harlos, K. / Stuart, D.I. / Barclay, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wng.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wng.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wng.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/2wng ftp://data.pdbj.org/pub/pdb/validation_reports/wn/2wng | 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: 36204.328 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 31-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEE14 / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Variant (production host): LEC3.2.8.1 / References: UniProt: P78324 |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
Sequence details | FINAL 8 RESIDUES (TRHHHHHH) ARE DERIVED FROM THE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6.5 Details: SITTING DROPS CONTAINING 100 NL SIRP (18.6 MG/ML) PLUS 100 NL PRECIPITANT (1.0 M TRI-SODIUM CITRATE, 0.1 M SODIUM CACODYLATE, PH 6.5) WERE EQUILIBRATED AT 20.5C AGAINST 95 UL RESERVOIRS OF ...Details: SITTING DROPS CONTAINING 100 NL SIRP (18.6 MG/ML) PLUS 100 NL PRECIPITANT (1.0 M TRI-SODIUM CITRATE, 0.1 M SODIUM CACODYLATE, PH 6.5) WERE EQUILIBRATED AT 20.5C AGAINST 95 UL RESERVOIRS OF PRECIPITANT. CRYSTALS WERE CRYO-PROTECTED BY A QUICK SWEEP THROUGH PERFLUOROPOLYETHER PFO-X125/03 (LANCASTER SYNTHESIS). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 27, 2007 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→38.1 Å / Num. obs: 14246 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 62.638 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.49→2.55 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2UV3, 2AJR AND 1ED3 Resolution: 2.49→27.05 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REMARK 3
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Displacement parameters | Biso mean: 62.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→27.05 Å
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LS refinement shell | Resolution: 2.49→2.64 Å / Total num. of bins used: 9
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