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- PDB-7nxd: Cryo-EM structure of human integrin alpha5beta1 in the half-bent ... -
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Basic information
Entry | Database: PDB / ID: 7nxd | |||||||||||||||||||||
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Title | Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation | |||||||||||||||||||||
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![]() | CELL ADHESION / integrin / plasma membrane protein / a5b1 / alpha5beta1 / focal adhesion / half-bent conformation | |||||||||||||||||||||
Function / homology | ![]() integrin alpha8-beta1 complex / myoblast fate specification / 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 / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process ...integrin alpha8-beta1 complex / myoblast fate specification / 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 / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / integrin alpha4-beta1 complex / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / cell-cell adhesion mediated by integrin / C-X3-C chemokine binding / integrin alpha1-beta1 complex / regulation of synapse pruning / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / reactive gliosis / cerebellar climbing fiber to Purkinje cell synapse / formation of radial glial scaffolds / Other semaphorin interactions / Formation of the ureteric bud / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / integrin alphav-beta1 complex / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / alphav-beta3 integrin-vitronectin complex / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / RUNX2 regulates genes involved in cell migration / MET interacts with TNS proteins / germ cell migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / Platelet Adhesion to exposed collagen / vascular endothelial growth factor receptor 2 binding / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / axon extension / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / myoblast differentiation / heterotypic cell-cell adhesion / integrin complex / positive regulation of cell-substrate adhesion / dendrite morphogenesis / Basigin interactions / Molecules associated with elastic fibres / muscle organ development / negative regulation of Rho protein signal transduction / lamellipodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / MET activates PTK2 signaling / negative regulation of vasoconstriction / cell adhesion mediated by integrin / Syndecan interactions / leukocyte cell-cell adhesion / epidermal growth factor receptor binding / positive regulation of wound healing / maintenance of blood-brain barrier / positive regulation of neuroblast proliferation / sarcomere organization / cell-substrate adhesion / positive regulation of sprouting angiogenesis / endodermal cell differentiation / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / cleavage furrow / glial cell projection / cellular response to low-density lipoprotein particle stimulus / fibronectin binding / 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 Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||||||||||||||
![]() | Schumacher, S. / Dedden, D. / Vazquez Nunez, R. / Matoba, K. / Takagi, J. / Biertumpfel, C. / Mizuno, N. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural insights into integrin αβ opening by fibronectin ligand. Authors: Stephanie Schumacher / Dirk Dedden / Roberto Vazquez Nunez / Kyoko Matoba / Junichi Takagi / Christian Biertümpfel / Naoko Mizuno / ![]() ![]() ![]() Abstract: Integrin αβ is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and αβ undergo conformational changes. While this is key for cell-tissue connections, ...Integrin αβ is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and αβ undergo conformational changes. While this is key for cell-tissue connections, its mechanism is unknown. Here, we report cryo-electron microscopy structures of native human αβ with fibronectin to 3.1-angstrom resolution, and in its resting state to 4.6-angstrom resolution. The αβ-fibronectin complex revealed simultaneous interactions at the arginine-glycine-aspartate loop, the synergy site, and a newly identified binding site proximal to adjacent to metal ion-dependent adhesion site, inducing the translocation of helix α1 to secure integrin opening. Resting αβ adopts an incompletely bent conformation, challenging the model of integrin sharp bending inhibiting ligand binding. Our biochemical and structural analyses showed that affinity of αβ for fibronectin is increased with manganese ions (Mn) while adopting the half-bent conformation, indicating that ligand-binding affinity does not depend on conformation, and αβ opening is induced by ligand-binding. | |||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 295.2 KB | Display | ![]() |
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PDB format | ![]() | 243.6 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 82.5 KB | Display | |
Data in CIF | ![]() | 115.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12637MC ![]() 7nwlC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 110111.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence used from GenBank entry CAA30790 / Source: (natural) ![]() |
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#2: Protein | Mass: 86338.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Sequence used from GenBank entry CAA30790 / Source: (natural) ![]() |
-Sugars , 5 types, 15 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: 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 #6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 8 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
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#7: Chemical | ChemComp-CA / #9: Chemical | ChemComp-MG / | |
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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 |
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Sample preparation
Component | Name: Dimeric complex of integrin a5b1 / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Value: 0.2 MDa / Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Integrin a5b1 was assembled into MSPE3D1 nanodiscs that contained bovine brain lipids (Folch fraction I) at a ratio of 1:29:3460, respectively. The assembly mix was incubated with SM-2 ...Details: Integrin a5b1 was assembled into MSPE3D1 nanodiscs that contained bovine brain lipids (Folch fraction I) at a ratio of 1:29:3460, respectively. The assembly mix was incubated with SM-2 BioBeads to remove DDM detergent from solubilized lipids and then purified by size-exclusion chromatography using a Superose 6 3.2/300 column. | |||||||||||||||||||||||||
Specimen support | Details: GloQube 20 mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() | |||||||||||||||
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3200 nm / Nominal defocus min: -500 nm / Cs: 2.62 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE | |||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | |||||||||||||||
Image recording | Imaging-ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
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EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: initial image processing automatically by FOCUS pipeline: gain normalization, motion correction and dose-weighting in MotionCor2 CTF estimation by GCTF | ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 496356 Details: 1424 particles were manually picked and used to obtain 2D classes with distinct features as templates for Gautomatch | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98750 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 386.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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