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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 | |||||||||
Components |
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Keywords | CELL ADHESION/IMMUNE SYSTEM / Integrin / Fv-clasp / Laminin / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex | |||||||||
| Function / homology | Function and homology informationintegrin alpha6-beta4 complex / integrin alpha8-beta1 complex / neuregulin binding / Type I hemidesmosome assembly / myoblast fate specification / integrin alpha3-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex ...integrin alpha6-beta4 complex / integrin alpha8-beta1 complex / neuregulin binding / Type I hemidesmosome assembly / myoblast fate specification / integrin alpha3-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 / integrin alpha5-beta1 complex / integrin alpha9-beta1 complex / ectodermal cell differentiation / cardiac cell fate specification / regulation of collagen catabolic process / nail development / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / cell adhesion receptor activity / integrin alpha4-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / cell-cell adhesion mediated by integrin / formation of radial glial scaffolds / Other semaphorin interactions / Formation of the ureteric bud / cerebellar climbing fiber to Purkinje cell synapse / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / myelin sheath abaxonal region / reactive gliosis / integrin alphav-beta1 complex / skin morphogenesis / CHL1 interactions / basement membrane organization / regulation of synapse pruning / cardiac muscle cell myoblast differentiation / Fibronectin matrix formation / MET interacts with TNS proteins / Laminin interactions / Platelet Adhesion to exposed collagen / Developmental Lineage of Mammary Stem Cells / primordial germ cell migration / leukocyte tethering or rolling / insulin-like growth factor I binding / myoblast fusion / cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / axon extension / cardiac muscle cell differentiation / cell-substrate junction assembly / myoblast differentiation / mesodermal cell differentiation / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / central nervous system neuron differentiation / cell projection organization / wound healing, spreading of epidermal cells / positive regulation of fibroblast migration / Assembly of collagen fibrils and other multimeric structures / negative regulation of Rho protein signal transduction / integrin complex / regulation of spontaneous synaptic transmission / cell adhesion mediated by integrin / MET activates PTK2 signaling / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / leukocyte migration / Basigin interactions / lamellipodium assembly / negative regulation of vasoconstriction / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / muscle organ development / Syndecan interactions / sarcomere organization / leukocyte cell-cell adhesion / dendrite morphogenesis / positive regulation of neuroblast proliferation / negative regulation of neuron differentiation / positive regulation of wound healing / response to muscle activity / cell-substrate adhesion / establishment of mitotic spindle orientation / maintenance of blood-brain barrier / homophilic cell-cell adhesion / Developmental Lineage of Mammary Gland Myoepithelial Cells / cleavage furrow / TGF-beta receptor signaling activates SMADs / fibronectin binding / negative regulation of anoikis / neuroblast proliferation / RHOG GTPase cycle / positive regulation of GTPase activity / intercalated disc / RAC3 GTPase cycle / RAC2 GTPase cycle / ECM proteoglycans Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human)![]() | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | |||||||||
Authors | Arimori, T. / Takagi, J. | |||||||||
| Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2021Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7ceb.cif.gz | 597 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb7ceb.ent.gz | 408.4 KB | Display | PDB format |
| PDBx/mmJSON format | 7ceb.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7ceb ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7ceb | HTTPS FTP |
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-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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Links
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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.) Homo sapiens (human) / Gene: ITGA6 / Production host: Homo sapiens (human) / References: UniProt: P23229 |
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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.) Homo sapiens (human) / Gene: ITGB1, FNRB, MDF2, MSK12 / Production host: Homo sapiens (human) / References: UniProt: P05556 |
-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.) ![]() Homo sapiens (human)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.) ![]() Homo sapiens (human)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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
| 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: MOLECULAR REPLACEMENTStarting 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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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group |
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Movie
Controller
About Yorodumi




Homo sapiens (human)
X-RAY DIFFRACTION
Japan, 2items
Citation














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