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Yorodumi- PDB-3vi4: Crystal structure of alpha5beta1 integrin headpiece in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 3vi4 | |||||||||
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Title | Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide | |||||||||
Components |
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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 information 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 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 / cell-cell adhesion mediated by integrin / C-X3-C chemokine binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / 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 / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / Formation of the ureteric bud / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / 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 / heterotypic cell-cell adhesion / myoblast differentiation / 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 / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / epidermal growth factor receptor binding / positive regulation of wound healing / maintenance of blood-brain barrier / sarcomere organization / positive regulation of neuroblast proliferation / cell-substrate adhesion / positive regulation of sprouting angiogenesis / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / homophilic cell adhesion via plasma membrane adhesion molecules / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / fibronectin binding / cellular response to low-density lipoprotein particle stimulus / 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 | Homo sapiens (human) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Nagae, M. / Nogi, T. / Takagi, J. | |||||||||
Citation | Journal: J.Cell Biol. / Year: 2012 Title: 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vi4.cif.gz | 574.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vi4.ent.gz | 466.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vi4_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3vi4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3vi4_validation.xml.gz | 102 KB | Display | |
Data in CIF | 3vi4_validation.cif.gz | 137.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/3vi4 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/3vi4 | HTTPS FTP |
-Related structure data
-Links
-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 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: Cricetulus griseus (Chinese hamster) / References: UniProt: P08648 #2: Protein | Mass: 50562.000 Da / Num. of mol.: 2 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: Cricetulus griseus (Chinese hamster) / References: UniProt: P05556 |
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-Protein/peptide , 1 types, 2 molecules GI
#5: Protein/peptide | Mass: 558.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence is found in fibronectin |
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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.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Mus musculus (house mouse) #4: Antibody | Mass: 23478.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): Hybridoma / Production host: Mus musculus (house mouse) |
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-Sugars , 3 types, 15 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | Source method: isolated from a genetically manipulated source #9: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 12 molecules
#8: Chemical | ChemComp-CA / #10: Chemical | |
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-Details
Sequence details | 1. THE SEQUENCE CONFLICTS OF ENTITY 2 ARE BASED ON REFERENCE 1 OF DATABASE UNIPROTKB/SWISS-PROT ...1. THE SEQUENCE CONFLICTS OF ENTITY 2 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/19SG/19 HEAVY CHAIN SG/19 HAS BEEN DEPOSITED TO EMBL WITH ACCESSION NUMBER HE578877. |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.27 % |
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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) PEG 8000, 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→116.45 Å / Num. all: 90587 / Num. obs: 89549 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.076 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.495 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→100 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.877 / SU B: 18.381 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / 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: 69.94 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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