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Open data
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Basic information
Entry | Database: PDB / ID: 1jlm | ||||||
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Title | I-DOMAIN FROM INTEGRIN CR3, MN2+ BOUND | ||||||
![]() | INTEGRIN | ||||||
![]() | CELL ADHESION PROTEIN / INTEGRIN / GLYCOPROTEIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, J.-O. / Liddington, R. | ||||||
![]() | ![]() Title: Two conformations of the integrin A-domain (I-domain): a pathway for activation? Authors: Lee, J.O. / Bankston, L.A. / Arnaout, M.A. / Liddington, R.C. #1: ![]() Title: Crystal Structure of the a Domain from the Alpha Subunit of Integrin Cr3 (Cd11B/Cd18) Authors: Lee, J.O. / Rieu, P. / Arnaout, M.A. / Liddington, R. #2: ![]() Title: A Novel Divalent Cation-Binding Site in the a Domain of the Beta 2 Integrin Cr3 (Cd11B/Cd18) is Essential for Ligand Binding Authors: Michishita, M. / Videm, V. / Arnaout, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418.3 KB | Display | ![]() |
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Full document | ![]() | 421.2 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1idoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21994.117 Da / Num. of mol.: 1 / Fragment: I-DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→12 Å / Num. obs: 12933 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.269 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1IDO Resolution: 2→12 Å / σ(F): 2
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Displacement parameters | Biso mean: 26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→12 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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