+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30342 | |||||||||
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Title | Structure of alpha6beta1 integrin in complex with laminin-511 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information laminin-5 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-11 complex / laminin-2 complex / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / integrin alpha6-beta1 complex / integrin alpha8-beta1 complex ...laminin-5 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-11 complex / laminin-2 complex / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / integrin alpha6-beta1 complex / integrin alpha8-beta1 complex / regulation of collagen catabolic process / 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 / integrin alpha9-beta1 complex / regulation of basement membrane organization / ectodermal cell differentiation / integrin alpha4-beta1 complex / neuregulin binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / cell-cell adhesion mediated by integrin / L1CAM interactions / integrin alpha1-beta1 complex / Type I hemidesmosome assembly / trunk neural crest cell migration / 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 / postsynapse organization / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / positive regulation of integrin-mediated signaling pathway / Formation of the ureteric bud / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / morphogenesis of embryonic epithelium / integrin alphav-beta1 complex / CD40 signaling pathway / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / morphogenesis of a polarized epithelium / myelin sheath abaxonal region / tissue development / germ cell migration / CHL1 interactions / cardiac muscle cell myoblast differentiation / skin morphogenesis / Laminin interactions / MET interacts with TNS proteins / leukocyte tethering or rolling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / cardiac muscle cell differentiation / endoderm development / cell projection organization / branching involved in salivary gland morphogenesis / Platelet Adhesion to exposed collagen / protein complex involved in cell-matrix adhesion / insulin-like growth factor I binding / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / regulation of epithelial cell proliferation / axon extension / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / positive regulation of fibroblast migration / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / myoblast differentiation / heterotypic cell-cell adhesion / lamellipodium assembly / integrin complex / regulation of spontaneous synaptic transmission / dendrite morphogenesis / odontogenesis / Basigin interactions / Molecules associated with elastic fibres / muscle organ development / negative regulation of Rho protein signal transduction / cell adhesion mediated by integrin / extracellular matrix structural constituent / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / sarcomere organization / branching involved in ureteric bud morphogenesis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Arimori T / Miyazaki N / Takagi J | |||||||||
Funding support | Japan, 2 items
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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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30342.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-30342-v30.xml emd-30342.xml | 25.5 KB 25.5 KB | Display Display | EMDB header |
Images | emd_30342.png | 123.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30342 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30342 | HTTPS FTP |
-Validation report
Summary document | emd_30342_validation.pdf.gz | 322.4 KB | Display | EMDB validaton report |
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Full document | emd_30342_full_validation.pdf.gz | 321.9 KB | Display | |
Data in XML | emd_30342_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_30342_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30342 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30342 | HTTPS FTP |
-Related structure data
Related structure data | 7cecMC 7ceaC 7cebC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30342.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.113 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 F...
+Supramolecule #1: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 F...
+Macromolecule #1: Integrin alpha-6
+Macromolecule #2: Integrin beta-1
+Macromolecule #3: Laminin subunit alpha-5
+Macromolecule #4: Laminin subunit beta-1
+Macromolecule #5: Laminin subunit gamma-1
+Macromolecule #6: TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH
+Macromolecule #7: TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C)
+Macromolecule #8: HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH
+Macromolecule #9: HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C)
+Macromolecule #11: CALCIUM ION
+Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #13: MANGANESE (II) ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.07 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: MOLYBDENUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 7768 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |