+Open data
-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 information integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / myoblast fate specification / positive regulation of glutamate uptake involved in transmission of nerve impulse / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha4-beta1 complex / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / ectodermal cell differentiation / neuregulin binding / Type I hemidesmosome assembly / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / nail development / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / formation of radial glial scaffolds / Other semaphorin interactions / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / CHL1 interactions / skin morphogenesis / cardiac muscle cell myoblast differentiation / Laminin interactions / germ cell migration / MET interacts with TNS proteins / leukocyte tethering or rolling / cardiac muscle cell differentiation / Platelet Adhesion to exposed collagen / cell projection organization / myoblast fusion / insulin-like growth factor I binding / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / axon extension / cell migration involved in sprouting angiogenesis / positive regulation of fibroblast migration / wound healing, spreading of epidermal cells / myoblast differentiation / heterotypic cell-cell adhesion / regulation of spontaneous synaptic transmission / integrin complex / dendrite morphogenesis / Basigin interactions / Molecules associated with elastic fibres / lamellipodium assembly / muscle organ development / sarcomere organization / negative regulation of Rho protein signal transduction / cell adhesion mediated by integrin / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / maintenance of blood-brain barrier / positive regulation of neuroblast proliferation / positive regulation of wound healing / leukocyte migration / cell-substrate adhesion / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / cellular response to low-density lipoprotein particle stimulus / fibronectin binding / neuroblast proliferation / RHOG GTPase cycle / intercalated disc / negative regulation of anoikis / negative regulation of neuron differentiation / ECM proteoglycans / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / laminin binding / cellular defense response / coreceptor activity / phagocytosis / positive regulation of phosphorylation / ruffle / RAC1 GTPase cycle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
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: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ceb.cif.gz | 596.1 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) |
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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.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) |
-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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-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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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