+Open data
-Basic information
Entry | Database: PDB / ID: 7cec | |||||||||
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Title | Structure of alpha6beta1 integrin in complex with laminin-511 | |||||||||
Components |
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Keywords | CELL ADHESION/IMMUNE SYSTEM / Integrin / Laminin / Fv-clasp / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / integrin alpha8-beta1 complex / integrin alpha3-beta1 complex ...laminin-5 complex / laminin-11 complex / laminin-2 complex / neuronal-glial interaction involved in cerebral cortex radial glia guided migration / laminin-8 complex / extracellular matrix of synaptic cleft / laminin-1 complex / laminin-10 complex / 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 / L1CAM interactions / integrin alpha1-beta1 complex / regulation of basement membrane organization / ectodermal cell differentiation / neuregulin binding / Type I hemidesmosome assembly / trunk neural crest cell migration / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / regulation of synapse pruning / hemidesmosome assembly / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / nail development / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / postsynapse organization / formation of radial glial scaffolds / Other semaphorin interactions / CD40 signaling pathway / positive regulation of integrin-mediated signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / morphogenesis of embryonic epithelium / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / morphogenesis of a polarized epithelium / tissue development / CHL1 interactions / skin morphogenesis / cardiac muscle cell myoblast differentiation / Laminin interactions / germ cell migration / MET interacts with TNS proteins / endoderm development / leukocyte tethering or rolling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / cardiac muscle cell differentiation / branching involved in salivary gland morphogenesis / Platelet Adhesion to exposed collagen / cell projection organization / myoblast fusion / protein complex involved in cell-matrix adhesion / insulin-like growth factor I binding / Elastic fibre formation / cell-substrate junction assembly / mesodermal cell differentiation / regulation of epithelial cell proliferation / 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 / odontogenesis / Molecules associated with elastic fibres / lamellipodium assembly / muscle organ development / sarcomere organization / negative regulation of Rho protein signal transduction / cell adhesion mediated by integrin / extracellular matrix structural constituent / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / branching involved in ureteric bud morphogenesis / maintenance of blood-brain barrier / positive regulation of neuroblast proliferation / positive regulation of wound healing Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Arimori, T. / Miyazaki, N. / 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7cec.cif.gz | 419.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cec.ent.gz | 330.3 KB | Display | PDB format |
PDBx/mmJSON format | 7cec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/7cec ftp://data.pdbj.org/pub/pdb/validation_reports/ce/7cec | HTTPS FTP |
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-Related structure data
Related structure data | 30342MC 7ceaC 7cebC M: map data used to model this data 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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-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 |
-Laminin subunit ... , 3 types, 3 molecules CDE
#3: Protein | Mass: 73414.203 Da / Num. of mol.: 1 / Fragment: E8 fragment / Mutation: I2723C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMA5, KIAA0533, KIAA1907 / Production host: Homo sapiens (human) / References: UniProt: O15230 |
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#4: Protein | Mass: 8552.753 Da / Num. of mol.: 1 / Fragment: E8 fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMB1 / Production host: Homo sapiens (human) / References: UniProt: P07942 |
#5: Protein | Mass: 9483.724 Da / Num. of mol.: 1 / Fragment: E8 fragment / Mutation: D1585C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LAMC1, LAMB2 / Production host: Homo sapiens (human) / References: UniProt: P11047 |
-Antibody , 4 types, 4 molecules FGHI
#6: 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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#7: 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) |
#8: Antibody | Mass: 19760.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of HUTS-4 VH(S112C)-SARAH Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) |
#9: Antibody | Mass: 17701.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimera of HUTS-4 VL(C87Y)-SARAH(S37C) Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) |
-Sugars , 2 types, 7 molecules
#10: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#12: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 7 molecules
#11: Chemical | ChemComp-CA / #13: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp Type: COMPLEX / Entity ID: #1-#9 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.286 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: MOLYBDENUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 800 nm / Nominal defocus min: 600 nm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7768 |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
Image scans | Width: 4096 / Height: 4096 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2660283 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 429521 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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