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- PDB-5mc9: Crystal structure of the heterotrimeric integrin-binding region o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mc9 | ||||||
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Title | Crystal structure of the heterotrimeric integrin-binding region of laminin-111 | ||||||
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![]() | CELL ADHESION / Extracellular matrix / coiled coil / laminin G-like domain | ||||||
Function / homology | ![]() laminin-3 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / retinal blood vessel morphogenesis ...laminin-3 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / laminin complex / laminin-1 complex / laminin-10 complex / tissue morphogenesis / hair follicle cell proliferation / retinal blood vessel morphogenesis / regulation of basement membrane organization / basement membrane assembly / morphogenesis of an epithelial sheet / hemidesmosome assembly / glycosphingolipid binding / positive regulation of integrin-mediated signaling pathway / tissue development / hair cell differentiation / branching involved in salivary gland morphogenesis / protein complex involved in cell-matrix adhesion / establishment of epithelial cell apical/basal polarity / negative regulation of cell adhesion / camera-type eye development / blood vessel morphogenesis / odontogenesis / extracellular matrix structural constituent / epithelial tube branching involved in lung morphogenesis / hair follicle morphogenesis / positive regulation of muscle cell differentiation / regulation of embryonic development / positive regulation of cell adhesion / basement membrane / extracellular matrix disassembly / synaptic cleft / regulation of cell migration / embryo implantation / substrate adhesion-dependent cell spreading / extracellular matrix / animal organ morphogenesis / axon guidance / neuromuscular junction / neuron projection development / cell-cell junction / cell migration / integrin binding / chromatin organization / retina development in camera-type eye / gene expression / protein-containing complex assembly / collagen-containing extracellular matrix / learning or memory / cell surface receptor signaling pathway / cell adhesion / positive regulation of cell migration / protein phosphorylation / signaling receptor binding / perinuclear region of cytoplasm / enzyme binding / extracellular space / extracellular region / membrane / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pulido, D. / Hohenester, E. | ||||||
![]() | ![]() Title: Crystal Structure of the Heterotrimeric Integrin-Binding Region of Laminin-111. Authors: Pulido, D. / Hussain, S.A. / Hohenester, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 409.6 KB | Display | ![]() |
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PDB format | ![]() | 336.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 442.2 KB | Display | |
Data in XML | ![]() | 27.6 KB | Display | |
Data in CIF | ![]() | 39.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wjsS 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: 69451.078 Da / Num. of mol.: 1 / Fragment: UNP residues 2079-2707 Source method: isolated from a genetically manipulated source Details: mouse laminin alpha1 chain, residues with disordered side chains are alanine Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 6451.335 Da / Num. of mol.: 1 / Fragment: UNP residues 1735-1786 Source method: isolated from a genetically manipulated source Details: mouse laminin beta1 chain, residues with disordered side chains are alanine Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Protein | Mass: 7179.124 Da / Num. of mol.: 1 / Fragment: UNP residues 1548-1607 Source method: isolated from a genetically manipulated source Details: mouse laminin gamma1 chain, residues with disordered side chains are alanine Source: (gene. exp.) ![]() ![]() ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.29 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.02 M magnesium chloride hexahydrate, 0.1 M Na-HEPES (pH 7.5), 22% w/v poly(acrylic acid sodium salt) 5100 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→56.9 Å / Num. obs: 47309 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.13→2.19 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.628 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WJS Resolution: 2.13→56.9 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→56.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 6.8846 Å / Origin y: -16.7014 Å / Origin z: -15.4714 Å
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Refinement TLS group | Selection details: all |