+Open data
-Basic information
Entry | Database: PDB / ID: 6om1 | |||||||||
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Title | Crystal structure of an atypical integrin | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Integrin / TGF-beta activation | |||||||||
Function / homology | Function and homology information ganglioside metabolic process / Langerhans cell differentiation / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding ...ganglioside metabolic process / Langerhans cell differentiation / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / Laminin interactions / placenta blood vessel development / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of phagocytosis / transforming growth factor beta binding / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of epidermal cells / cartilage development / apoptotic cell clearance / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / cell adhesion mediated by integrin / microvillus membrane / Syndecan interactions / negative chemotaxis / cell-substrate adhesion / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / fibronectin binding / positive regulation of cell adhesion / ECM proteoglycans / voltage-gated calcium channel activity / vasculogenesis / Integrin cell surface interactions / specific granule membrane / coreceptor activity / phagocytic vesicle / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / substrate adhesion-dependent cell spreading / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / protein kinase C binding / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / calcium ion transmembrane transport / response to virus / cell-cell adhesion / ruffle membrane / VEGFA-VEGFR2 Pathway / positive regulation of angiogenesis / cell migration / integrin binding / virus receptor activity / positive regulation of cytosolic calcium ion concentration / angiogenesis / protease binding / cell adhesion / positive regulation of cell migration / immune response / symbiont entry into host cell / external side of plasma membrane / negative regulation of gene expression / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å | |||||||||
Authors | Wang, J.C. / Springer, T.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: General structural features that regulate integrin affinity revealed by atypical alpha V beta 8. Authors: Wang, J. / Su, Y. / Iacob, R.E. / Engen, J.R. / Springer, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6om1.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6om1.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 6om1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/6om1 ftp://data.pdbj.org/pub/pdb/validation_reports/om/6om1 | HTTPS FTP |
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-Related structure data
Related structure data | 6om2C 4um9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 65738.719 Da / Num. of mol.: 4 / Mutation: M400GC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Plasmid: pcDNA3.1 / Details (production host): Hygromycin resistance / Cell line (production host): HEK293s Gnt1 -/- / Production host: Homo sapiens (human) / Strain (production host): HEK293 / References: UniProt: P06756 #2: Protein | Mass: 50661.445 Da / Num. of mol.: 4 / Mutation: V301C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB8 / Production host: Homo sapiens (human) / References: UniProt: P26012 |
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-Sugars , 8 types, 37 molecules
#3: 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 #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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 #6: 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 #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-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 #9: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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 #10: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 472 molecules
#11: Chemical | ChemComp-CA / #12: Chemical | ChemComp-EDO / #13: Chemical | ChemComp-MG / #14: Chemical | ChemComp-MES / #15: Water | ChemComp-HOH / | |
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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: 3.13 Å3/Da / Density % sol: 60.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 100 mM MES, pH 6.7, 12% PEG 20000 / PH range: 6.3 - 6.7 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→48.072 Å / Num. obs: 141394 / % possible obs: 95.5 % / Redundancy: 1.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.133 / Net I/σ(I): 5.87 |
Reflection shell | Resolution: 2.66→2.73 Å / Redundancy: 1.7 % / Num. unique obs: 10550 / CC1/2: 0.199 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UM9 Resolution: 2.66→48.072 Å / Cross valid method: FREE R-VALUE / σ(F): 3.18 / Phase error: 39.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.66→48.072 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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