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Open data
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Basic information
Entry | Database: PDB / ID: 7ceb | |||||||||
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Title | Crystal structure of alpha6beta1 integrin headpiece | |||||||||
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![]() | CELL ADHESION/IMMUNE SYSTEM / Integrin / Fv-clasp / Laminin / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() integrin alpha6-beta4 complex / ectodermal cell differentiation / integrin alpha8-beta1 complex / neuregulin binding / Type I hemidesmosome assembly / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex ...integrin alpha6-beta4 complex / ectodermal cell differentiation / integrin alpha8-beta1 complex / neuregulin binding / Type I hemidesmosome assembly / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / nail development / collagen binding involved in cell-matrix adhesion / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / integrin alpha2-beta1 complex / : / reactive gliosis / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / myelin sheath abaxonal region / CD40 signaling pathway / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / integrin alphav-beta1 complex / regulation of synapse pruning / skin morphogenesis / basement membrane organization / CHL1 interactions / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / Laminin interactions / leukocyte tethering or rolling / cardiac muscle cell differentiation / germ cell migration / Platelet Adhesion to exposed collagen / cell projection organization / insulin-like growth factor I binding / central nervous system neuron differentiation / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / myoblast differentiation / cell migration involved in sprouting angiogenesis / axon extension / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / positive regulation of cell-substrate adhesion / integrin complex / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / regulation of spontaneous synaptic transmission / lamellipodium assembly / Assembly of collagen fibrils and other multimeric structures / sarcomere organization / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / leukocyte migration / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / maintenance of blood-brain barrier / muscle organ development / Syndecan interactions / positive regulation of wound healing / dendrite morphogenesis / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / response to muscle activity / cell-substrate adhesion / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / cleavage furrow / establishment of mitotic spindle orientation / fibronectin binding / negative regulation of anoikis / cellular response to low-density lipoprotein particle stimulus / intercalated disc / RHOG GTPase cycle / positive regulation of phosphorylation / glial cell projection / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of neuron differentiation Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Arimori, T. / Takagi, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanism of laminin recognition by integrin. Authors: Takao Arimori / Naoyuki Miyazaki / Emiko Mihara / Mamoru Takizawa / Yukimasa Taniguchi / Carlos Cabañas / Kiyotoshi Sekiguchi / Junichi Takagi / ![]() ![]() Abstract: Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we ...Recognition of laminin by integrin receptors is central to the epithelial cell adhesion to basement membrane, but the structural background of this molecular interaction remained elusive. Here, we report the structures of the prototypic laminin receptor α6β1 integrin alone and in complex with three-chain laminin-511 fragment determined via crystallography and cryo-electron microscopy, respectively. The laminin-integrin interface is made up of several binding sites located on all five subunits, with the laminin γ1 chain C-terminal portion providing focal interaction using two carboxylate anchor points to bridge metal-ion dependent adhesion site of integrin β1 subunit and Asn189 of integrin α6 subunit. Laminin α5 chain also contributes to the affinity and specificity by making electrostatic interactions with large surface on the β-propeller domain of α6, part of which comprises an alternatively spliced X1 region. The propeller sheet corresponding to this region shows unusually high mobility, suggesting its unique role in ligand capture. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 597 KB | Display | ![]() |
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PDB format | ![]() | 408.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 493.5 KB | Display | ![]() |
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Full document | ![]() | 511.6 KB | Display | |
Data in XML | ![]() | 43.3 KB | Display | |
Data in CIF | ![]() | 58.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ceaC ![]() 7cecC ![]() 3vi3S ![]() 4wk0S ![]() 5xcxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 69776.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 50510.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 19463.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of TS2/16 VH(S112C)-SARAH Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() |
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#4: Antibody | Mass: 18270.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of TS2/16 VL-SARAH(S37C) Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() |
-Sugars , 1 types, 6 molecules 
#6: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 8 molecules 




#5: Chemical | ChemComp-CA / #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 23% PEG1000, 0.2 M NaCl, 0.1 M Na/K phosphate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→47.8 Å / Num. obs: 42251 / % possible obs: 99.6 % / Redundancy: 9.75 % / Biso Wilson estimate: 72.74 Å2 / CC1/2: 0.997 / Rsym value: 0.158 / Net I/σ(I): 12.48 |
Reflection shell | Resolution: 2.89→3.07 Å / Mean I/σ(I) obs: 1.63 / Num. unique obs: 6580 / CC1/2: 0.806 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4wk0, 3vi3, 5xcx Resolution: 2.89→44.57 Å / SU ML: 0.402 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3919 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→44.57 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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