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Yorodumi- PDB-3vi3: Crystal structure of alpha5beta1 integrin headpiece (ligand-free form) -
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Open data
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Basic information
| Entry | Database: PDB / ID: 3vi3 | |||||||||
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| Title | Crystal structure of alpha5beta1 integrin headpiece (ligand-free form) | |||||||||
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Keywords | CELL ADHESION/IMMUNE SYSTEM / beta propeller fold / Rossmann fold / beta sandwich / Fibronectin receptor / CELL ADHESION-IMMUNE SYSTEM complex | |||||||||
| 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 / Molecules associated with elastic fibres / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / muscle organ development / cell adhesion mediated by integrin / Syndecan interactions / 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Nagae, M. / Nogi, T. / Takagi, J. | |||||||||
Citation | Journal: J.Cell Biol. / Year: 2012Title: Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor Authors: Nagae, M. / Re, S. / Mihara, E. / Nogi, T. / Sugita, Y. / Takagi, J. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 3vi3.cif.gz | 577.7 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb3vi3.ent.gz | 465.3 KB | Display | PDB format |
| PDBx/mmJSON format | 3vi3.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 3vi3_validation.pdf.gz | 831.8 KB | Display | wwPDB validaton report |
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| Full document | 3vi3_full_validation.pdf.gz | 885.5 KB | Display | |
| Data in XML | 3vi3_validation.xml.gz | 113.6 KB | Display | |
| Data in CIF | 3vi3_validation.cif.gz | 145.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/3vi3 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3vi3 | HTTPS FTP |
-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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| Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
| #1: Protein | Mass: 68188.523 Da / Num. of mol.: 2 / Fragment: UNP residues 42-664 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FNRA, ITGA5 / Cell (production host): CHO-lec3.2.8.1 cell / Production host: ![]() #2: Protein | Mass: 50562.000 Da / Num. of mol.: 2 / Fragment: UNP residues 21-465 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FNRB, ITGB1, MDF2, MSK12 / Cell (production host): CHO-lec3.2.8.1 cell / Production host: ![]() |
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-Antibody , 2 types, 4 molecules LEHF
| #3: Antibody | Mass: 24216.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 23478.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 15 molecules 
| #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 14 molecules 


| #7: Chemical | ChemComp-CA / #9: Chemical | |
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-Details
| Has protein modification | Y |
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| Sequence details | 1. THE SEQUENCE CONFLICTS OF ENTITY 2 (INTEGRIN BETA-1) ARE BASED ON REFERENCE 1 OF DATABASE ...1. THE SEQUENCE CONFLICTS OF ENTITY 2 (INTEGRIN BETA-1) ARE BASED ON REFERENCE 1 OF DATABASE UNIPROTKB/SWISS-PROT P05556 (ITB1_HUMAN). 2. THE SEQUENCE OF SG/19 LIGHT CHAIN HAS BEEN DEPOSITED TO EMBL WITH ACCESSION NUMBER HE578878, AND SG/19 HEAVY CHAIN SG/19 HAS BEEN DEPOSITED TO EMBL WITH ACCESSION NUMBER HE578877. |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.13 % |
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| Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-tris (pH6.5), 20%(w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
| Diffraction | Mean temperature: 90 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9 Å |
| Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2010 / Details: mirrors |
| Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
| Reflection | Resolution: 2.9→116.39 Å / Num. all: 91525 / Num. obs: 90446 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rsym value: 0.061 / Net I/σ(I): 11.5 |
| Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.462 / % possible all: 98.3 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→100 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 17.896 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 71.736 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.9→100 Å
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| Refine LS restraints |
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| LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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Homo sapiens (human)
X-RAY DIFFRACTION
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