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Open data
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Basic information
Entry | Database: PDB / ID: 1dzi | ||||||
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Title | integrin alpha2 I domain / collagen complex | ||||||
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![]() | INTEGRIN / COLLAGEN | ||||||
Function / homology | ![]() collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid / CHL1 interactions ...collagen receptor activity / substrate-dependent cell migration / positive regulation of transmission of nerve impulse / positive regulation of cell projection organization / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / response to parathyroid hormone / hypotonic response / response to L-ascorbic acid / CHL1 interactions / Laminin interactions / skin morphogenesis / basal part of cell / positive regulation of smooth muscle contraction / positive regulation of phagocytosis, engulfment / collagen-activated signaling pathway / mammary gland development / Platelet Adhesion to exposed collagen / hepatocyte differentiation / mesodermal cell differentiation / focal adhesion assembly / heparan sulfate proteoglycan binding / integrin complex / response to muscle activity / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cell adhesion mediated by integrin / MET activates PTK2 signaling / Syndecan interactions / cell-substrate adhesion / positive regulation of epithelial cell migration / positive regulation of smooth muscle cell migration / response to amine / positive regulation of cell adhesion / ECM proteoglycans / positive regulation of collagen biosynthetic process / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / axon terminus / laminin binding / collagen binding / extracellular matrix organization / cell-matrix adhesion / cellular response to estradiol stimulus / integrin-mediated signaling pathway / positive regulation of translation / female pregnancy / animal organ morphogenesis / positive regulation of smooth muscle cell proliferation / cell-cell adhesion / cellular response to mechanical stimulus / blood coagulation / integrin binding / virus receptor activity / amyloid-beta binding / response to hypoxia / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Emsley, j. / Knight, G. / Farndale, R. / Barnes, M. / Liddington, R. | ||||||
![]() | ![]() Title: Structural Basis of Collagen Recognition by Integrin Alpha2Beta1 Authors: Emsley, J. / Knight, G. / Farndale, R. / Barnes, M. / Liddington, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.9 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20359.053 Da / Num. of mol.: 1 / Fragment: ALPHA2 I DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 2013.130 Da / Num. of mol.: 3 / Fragment: TRIMERIC GPOGPOGFOGERGPOGPOGPO 21MERIC PEPTIDE / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-CO / | #4: Water | ChemComp-HOH / | Sequence details | CHAIN A: C-TERMINAL ALA IS A SER IN ITA2_HUMAN | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.19 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / 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: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 14483 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 12 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.9 |
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Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Software | *PLUS Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.203 / Rfactor Rfree: 0.2729 / Rfactor Rwork: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |