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Yorodumi- PDB-1m1u: AN ISOLEUCINE-BASED ALLOSTERIC SWITCH CONTROLS AFFINITY AND SHAPE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m1u | ||||||
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Title | AN ISOLEUCINE-BASED ALLOSTERIC SWITCH CONTROLS AFFINITY AND SHAPE SHIFTING IN INTEGRIN CD11B A-DOMAIN | ||||||
Components | Integrin alpha-M | ||||||
Keywords | CELL ADHESION / INTEGRIN / CELL ADHESION PROTEIN / GLYCOPROTEIN / A-domain / CD11b | ||||||
Function / homology | Function and homology information ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning ...ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / complement receptor mediated signaling pathway / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / cell adhesion mediated by integrin / phagocytosis, engulfment / amyloid-beta clearance / plasma membrane raft / tertiary granule membrane / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / response to mechanical stimulus / forebrain development / heat shock protein binding / cell-matrix adhesion / receptor-mediated endocytosis / positive regulation of superoxide anion generation / response to ischemia / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / integrin binding / response to estradiol / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / external side of plasma membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Xiong, J.-P. / Li, R. / Essafi, M. / Stehle, T. / Arnaout, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: An isoleucine-based allosteric switch controls affinity and shape shifting in integrin CD11b A-domain. Authors: Xiong, J.P. / Li, R. / Essafi, M. / Stehle, T. / Arnaout, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m1u.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m1u.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 1m1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m1u_validation.pdf.gz | 365.9 KB | Display | wwPDB validaton report |
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Full document | 1m1u_full_validation.pdf.gz | 367.9 KB | Display | |
Data in XML | 1m1u_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 1m1u_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m1u ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m1u | HTTPS FTP |
-Related structure data
Related structure data | 1idoS S: Starting model for refinement |
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Similar 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: 22261.314 Da / Num. of mol.: 1 / Fragment: CD11b A-domain, Residues 123-315 / Mutation: C128S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P11215 |
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#2: Chemical | ChemComp-CA / |
#3: 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: 2.22 Å3/Da / Density % sol: 44.66 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 15% PEG8K, 0.1M Tris-HCl 8.2, 5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
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: X12B / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 1999 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→8 Å / Num. obs: 7963 / % possible obs: 91.1 % / Observed criterion σ(I): -2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 |
Reflection | *PLUS Num. obs: 7955 / Redundancy: 2.3 % / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 80.8 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1IDO Resolution: 2.3→8 Å / Cross valid method: througthout / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.188 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS |