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Yorodumi- 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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Keywords | CELL ADHESION / integrin / plasma membrane protein / a5b1 / alpha5beta1 / focal adhesion / half-bent conformation | |||||||||||||||||||||
| Function / homology | Function and homology informationintegrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-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 / integrin alpha9-beta1 complex ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-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 / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / myelin sheath abaxonal region / CD40 signaling pathway / calcium-independent cell-matrix adhesion / Fibronectin matrix formation / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of synapse pruning / integrin alphav-beta1 complex / CHL1 interactions / basement membrane organization / RUNX2 regulates genes involved in cell migration / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / alphav-beta3 integrin-vitronectin complex / Laminin interactions / cardiac muscle cell differentiation / Platelet Adhesion to exposed collagen / germ cell migration / leukocyte tethering or rolling / vascular endothelial growth factor receptor 2 binding / cell projection organization / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / positive regulation of vascular endothelial growth factor receptor signaling pathway / central nervous system neuron differentiation / positive regulation of cell-substrate adhesion / regulation of spontaneous synaptic transmission / heterophilic cell-cell adhesion / wound healing, spreading of epidermal cells / epidermal growth factor receptor binding / positive regulation of fibroblast migration / integrin complex / lamellipodium assembly / sarcomere organization / heterotypic cell-cell adhesion / MET activates PTK2 signaling / Basigin interactions / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / muscle organ development / Syndecan interactions / cell adhesion mediated by integrin / positive regulation of wound healing / dendrite morphogenesis / negative regulation of neuron differentiation / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / response to muscle activity / maintenance of blood-brain barrier / positive regulation of sprouting angiogenesis / cell-substrate adhesion / homophilic cell-cell adhesion / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / cleavage furrow / establishment of mitotic spindle orientation / fibronectin binding / negative regulation of anoikis / intercalated disc / cellular response to low-density lipoprotein particle stimulus / positive regulation of GTPase activity / RHOG GTPase cycle / glial cell projection / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / ECM proteoglycans Similarity search - Function | |||||||||||||||||||||
| Biological species | Homo sapiens (human) | |||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||||||||||||||
Authors | Schumacher, S. / Dedden, D. / Vazquez Nunez, R. / Matoba, K. / Takagi, J. / Biertumpfel, C. / Mizuno, N. | |||||||||||||||||||||
| Funding support | Germany, European Union, United States, 6items
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Citation | Journal: Sci Adv / Year: 2021Title: 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. | |||||||||||||||||||||
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Structure visualization
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| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7nxd.cif.gz | 303.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb7nxd.ent.gz | 239.1 KB | Display | PDB format |
| PDBx/mmJSON format | 7nxd.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7nxd_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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| Full document | 7nxd_full_validation.pdf.gz | 2 MB | Display | |
| Data in XML | 7nxd_validation.xml.gz | 82.1 KB | Display | |
| Data in CIF | 7nxd_validation.cif.gz | 115.4 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/7nxd ftp://data.pdbj.org/pub/pdb/validation_reports/nx/7nxd | 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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Links
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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) Homo sapiens (human) / Tissue: placenta / References: UniProt: P08648 |
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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) Homo sapiens (human) / Tissue: placenta / References: UniProt: P05556 |
-Sugars , 5 types, 15 molecules 
| #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 


| #7: Chemical | ChemComp-CA / #9: Chemical | ChemComp-MG / | |
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-Details
| Has ligand of interest | N |
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| Has protein modification | Y |
-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: Homo sapiens (human) | |||||||||||||||||||||||||
| Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
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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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | |||||||||||||||
| 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 | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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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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About Yorodumi



Homo sapiens (human)
Germany, European Union,
United States, 6items
Citation
UCSF Chimera













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