+Open data
-Basic information
Entry | Database: PDB / ID: 1ido | ||||||
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Title | I-DOMAIN FROM INTEGRIN CR3, MG2+ BOUND | ||||||
Components | INTEGRIN | ||||||
Keywords | CELL ADHESION PROTEIN / INTEGRIN / GLYCOPROTEIN / EXTRACELLULAR MATRIX / CYTOSKELETON | ||||||
Function / homology | Function and homology information ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / 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 / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / 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 / receptor-mediated endocytosis / cell-matrix adhesion / 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 / MAD SOFTWARE USED : MLPHARE STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 1.7 Å | ||||||
Authors | Lee, J.-O. / Liddington, R. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1995 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. #1: Journal: Structure / Year: 1995 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. #2: Journal: Cell(Cambridge,Mass.) / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ido.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ido.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ido.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/1ido ftp://data.pdbj.org/pub/pdb/validation_reports/id/1ido | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21662.705 Da / Num. of mol.: 1 / Fragment: I-DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: P11215 |
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#2: Chemical | ChemComp-MG / |
#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: 2.27 Å3/Da / Density % sol: 45.86 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9300, 0.9686, 0.9793, 0.9797 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE | |||||||||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→12 Å / Num. obs: 21824 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.046 | |||||||||||||||
Reflection shell | Resolution: 1.71→1.78 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.25 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD SOFTWARE USED : MLPHARE STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL Resolution: 1.7→7 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.7→7 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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