+Open data
-Basic information
Entry | Database: PDB / ID: 5xau | |||||||||
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Title | Crystal structure of integrin binding fragment of laminin-511 | |||||||||
Components | (Laminin subunit ...) x 3 | |||||||||
Keywords | CELL ADHESION / laminin / integrin / extracellular matrix protein | |||||||||
Function / homology | Function and homology information laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / L1CAM interactions / regulation of basement membrane organization ...laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / L1CAM interactions / regulation of basement membrane organization / trunk neural crest cell migration / hemidesmosome assembly / postsynapse organization / positive regulation of integrin-mediated signaling pathway / morphogenesis of embryonic epithelium / morphogenesis of a polarized epithelium / tissue development / Laminin interactions / endoderm development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / branching involved in salivary gland morphogenesis / protein complex involved in cell-matrix adhesion / regulation of epithelial cell proliferation / muscle organ development / odontogenesis / extracellular matrix structural constituent / MET activates PTK2 signaling / maintenance of blood-brain barrier / branching involved in ureteric bud morphogenesis / endodermal cell differentiation / positive regulation of muscle cell differentiation / odontogenesis of dentin-containing tooth / regulation of embryonic development / Non-integrin membrane-ECM interactions / cilium assembly / basement membrane / positive regulation of cell adhesion / hair follicle development / ECM proteoglycans / extracellular matrix disassembly / synaptic cleft / regulation of cell adhesion / regulation of cell migration / Degradation of the extracellular matrix / substrate adhesion-dependent cell spreading / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / axon guidance / protein localization to plasma membrane / Post-translational protein phosphorylation / lung development / animal organ morphogenesis / neuromuscular junction / cell-cell adhesion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cell migration / integrin binding / collagen-containing extracellular matrix / protein-containing complex assembly / Interleukin-4 and Interleukin-13 signaling / cell adhesion / positive regulation of cell migration / endoplasmic reticulum lumen / glutamatergic synapse / structural molecule activity / perinuclear region of cytoplasm / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||
Authors | Takizawa, M. / Arimori, T. / Kitago, Y. / Takagi, J. / Sekiguchi, K. | |||||||||
Citation | Journal: Sci Adv / Year: 2017 Title: Mechanistic basis for the recognition of laminin-511 by alpha 6 beta 1 integrin. Authors: Takizawa, M. / Arimori, T. / Taniguchi, Y. / Kitago, Y. / Yamashita, E. / Takagi, J. / Sekiguchi, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xau.cif.gz | 591.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xau.ent.gz | 486 KB | Display | PDB format |
PDBx/mmJSON format | 5xau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xa/5xau ftp://data.pdbj.org/pub/pdb/validation_reports/xa/5xau | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Laminin subunit ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 73414.203 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2655-3327 / Mutation: I2723C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMA5, KIAA0533, KIAA1907 / Production host: Homo sapiens (human) / References: UniProt: O15230 #2: Protein | Mass: 8552.753 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1714-1786 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMB1 / Production host: Homo sapiens (human) / References: UniProt: P07942 #3: Protein | Mass: 9483.724 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1528-1609 / Mutation: D1585C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMC1, LAMB2 / Production host: Homo sapiens (human) / References: UniProt: P11047 |
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-Sugars , 2 types, 8 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 593 molecules
#5: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate (pH 4.2), 19% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 164205 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rsym value: 0.065 / Net I/σ(I): 29.08 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.47 / Rsym value: 1.14 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→49.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.081 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.64 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→49.41 Å
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