+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 / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / 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 / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / ectodermal cell differentiation / C-X3-C chemokine binding / neuregulin binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / Type I hemidesmosome assembly / nail development / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of synapse pruning / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / Formation of the ureteric bud / 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 / skin morphogenesis / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / MET interacts with TNS proteins / germ cell migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / Platelet Adhesion to exposed collagen / insulin-like growth factor I binding / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / axon extension / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / dendrite morphogenesis / Basigin interactions / Molecules associated with elastic fibres / muscle organ development / negative regulation of Rho protein signal transduction / lamellipodium assembly / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / positive regulation of wound healing / maintenance of blood-brain barrier / sarcomere organization / positive regulation of neuroblast proliferation / leukocyte migration / cell-substrate adhesion / TGF-beta receptor signaling activates SMADs / homophilic cell adhesion via plasma membrane adhesion molecules / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / fibronectin binding / cellular response to low-density lipoprotein particle stimulus / negative regulation of anoikis / intercalated disc / RHOG GTPase cycle / negative regulation of neuron differentiation / ECM proteoglycans / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / cellular defense response / coreceptor activity / phagocytosis / laminin binding / positive regulation of phosphorylation 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
Summary document | 7ceb_validation.pdf.gz | 493.5 KB | Display | wwPDB validaton report |
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Full document | 7ceb_full_validation.pdf.gz | 511.6 KB | Display | |
Data in XML | 7ceb_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 7ceb_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7ceb ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7ceb | HTTPS FTP |
-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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