+
Open data
-
Basic information
Entry | Database: PDB / ID: 7cec | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of alpha6beta1 integrin in complex with laminin-511 | |||||||||
![]() |
| |||||||||
![]() | CELL ADHESION/IMMUNE SYSTEM / Integrin / Laminin / Fv-clasp / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() 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 / 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 / regulation of basement membrane organization / 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 / L1CAM interactions / integrin alpha1-beta1 complex / Type I hemidesmosome assembly / trunk neural crest cell migration / basement membrane assembly / 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 / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / morphogenesis of embryonic epithelium / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / morphogenesis of a polarized epithelium / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / tissue development / skin morphogenesis / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / MET interacts with TNS proteins / germ cell migration / EGR2 and SOX10-mediated initiation of Schwann cell myelination / leukocyte tethering or rolling / endoderm development / cardiac muscle cell differentiation / branching involved in salivary gland morphogenesis / cell projection organization / 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 / 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 / odontogenesis / 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 / extracellular matrix structural constituent / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of wound healing Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Arimori, T. / Miyazaki, N. / Takagi, J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 419.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 330.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 844.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 887.7 KB | Display | |
Data in XML | ![]() | 67.7 KB | Display | |
Data in CIF | ![]() | 102.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30342MC ![]() 7ceaC ![]() 7cebC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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.) ![]() ![]() |
---|---|
#2: Protein | Mass: 50510.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-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.) ![]() ![]() |
---|---|
#4: Protein | Mass: 8552.753 Da / Num. of mol.: 1 / Fragment: E8 fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#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.) ![]() ![]() |
-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.) ![]() ![]() ![]() Production host: ![]() ![]() |
---|---|
#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.) ![]() ![]() ![]() Production host: ![]() ![]() |
#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.) ![]() ![]() ![]() Production host: ![]() ![]() |
#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.) ![]() ![]() ![]() Production host: ![]() ![]() |
-Sugars , 2 types, 7 molecules ![](data/chem/img/NAG.gif)
#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 |
---|---|
#12: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 7 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MN.gif)
#11: Chemical | ChemComp-CA / #13: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
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 | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.286 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / 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 |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||
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 |
|