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Yorodumi- EMDB-3635: Localised Reconstruction of Integrin alpha V beta 6 bound to Foot... -
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-Basic information
Entry | Database: EMDB / ID: EMD-3635 | |||||||||
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Title | Localised Reconstruction of Integrin alpha V beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B. | |||||||||
Map data | Localised Reconstruction of Integrin alpha v beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B | |||||||||
Sample |
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Function / homology | Function and homology information Langerhans cell differentiation / icosahedral viral capsid / 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 ...Langerhans cell differentiation / icosahedral viral capsid / 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) / bronchiole development / enamel mineralization / extracellular matrix protein binding / modulation by virus of host chromatin organization / Laminin interactions / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / phospholipid homeostasis / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / regulation of phagocytosis / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / surfactant homeostasis / filopodium membrane / positive regulation of small GTPase mediated signal transduction / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of epidermal cells / 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 / skin development / microvillus membrane / Syndecan interactions / negative chemotaxis / lung alveolus development / 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 / ribonucleoside triphosphate phosphatase activity / substrate adhesion-dependent cell spreading / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / protein kinase C binding / Signal transduction by L1 / T=pseudo3 icosahedral viral capsid / molecular function activator activity / integrin-mediated signaling pathway / cellular response to ionizing radiation / host cell cytoplasmic vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway / calcium ion transmembrane transport / response to virus / wound healing / bone development / cytoplasmic vesicle membrane / cell morphogenesis / cell-cell adhesion / ruffle membrane / VEGFA-VEGFR2 Pathway / : / cell migration / integrin binding / regulation of translation / virus receptor activity / protein complex oligomerization / cell junction / monoatomic ion channel activity / positive regulation of cytosolic calcium ion concentration / clathrin-dependent endocytosis of virus by host cell / angiogenesis / protease binding / host cell cytoplasm / RNA helicase activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Foot-and-mouth disease virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.3 Å | |||||||||
Authors | Kotecha A / Stuart D | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Rules of engagement between αvβ6 integrin and foot-and-mouth disease virus. Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T ...Authors: Abhay Kotecha / Quan Wang / Xianchi Dong / Serban L Ilca / Marina Ondiviela / Rao Zihe / Julian Seago / Bryan Charleston / Elizabeth E Fry / Nicola G A Abrescia / Timothy A Springer / Juha T Huiskonen / David I Stuart / Abstract: Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, ...Foot-and-mouth disease virus (FMDV) mediates cell entry by attachment to an integrin receptor, generally αvβ6, via a conserved arginine-glycine-aspartic acid (RGD) motif in the exposed, antigenic, GH loop of capsid protein VP1. Infection can also occur in tissue culture adapted virus in the absence of integrin via acquired basic mutations interacting with heparin sulphate (HS); this virus is attenuated in natural infections. HS interaction has been visualized at a conserved site in two serotypes suggesting a propensity for sulfated-sugar binding. Here we determined the interaction between αvβ6 and two tissue culture adapted FMDV strains by cryo-electron microscopy. In the preferred mode of engagement, the fully open form of the integrin, hitherto unseen at high resolution, attaches to an extended GH loop via interactions with the RGD motif plus downstream hydrophobic residues. In addition, an N-linked sugar of the integrin attaches to the previously identified HS binding site, suggesting a functional role. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3635.map.gz | 7.2 MB | EMDB map data format | |
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Header (meta data) | emd-3635-v30.xml emd-3635.xml | 24 KB 24 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3635_fsc.xml | 4.5 KB | Display | FSC data file |
Images | emd_3635.png | 115.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3635 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3635 | HTTPS FTP |
-Related structure data
Related structure data | 5neuMC 3630C 3631C 3632C 3633C 3634C 5ne4C 5nedC 5nejC 5nemC 5nerC 5netC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3635.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Localised Reconstruction of Integrin alpha v beta 6 bound to Foot and Mouth Disease Virus O1 Manisa - Pose B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Foot-and-mouth disease virus
+Supramolecule #1: Foot-and-mouth disease virus
+Supramolecule #3: Integrin
+Supramolecule #2: Foot-and-mouth disease virus
+Macromolecule #1: O1 Manisa VP1
+Macromolecule #2: O1 Manisa VP2
+Macromolecule #3: Capsid protein
+Macromolecule #4: O1 Manisa VP4
+Macromolecule #5: Integrin alpha-V
+Macromolecule #6: Integrin beta-6
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: CALCIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Component - Concentration: 50.0 mM / Component - Name: HEPES |
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 160000 |
Specialist optics | Energy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Sample stage | Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 360 / Average exposure time: 5.0 sec. / Average electron dose: 18.0 e/Å2 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 120 / Target criteria: Cross-correlation coefficient |
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Output model | PDB-5neu: |