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Yorodumi- EMDB-3632: Localised reconstruction of alpha v beta 6 bound to Foot and Mout... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3632 | ||||||||||||
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Title | Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O PanAsia - Pose A. | ||||||||||||
Map data | Localised reconstruction of alpha v beta 6 bound to FMDV O PanAsia - Pose A | ||||||||||||
Sample |
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Function / homology | Function and homology information icosahedral viral capsid / 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 ...icosahedral viral capsid / 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) / enamel mineralization / extracellular matrix protein binding / modulation by virus of host chromatin organization / bronchiole development / RNA-protein covalent cross-linking / Laminin interactions / 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 / phospholipid homeostasis / : / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / regulation of phagocytosis / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / surfactant homeostasis / filopodium membrane / extracellular matrix binding / positive regulation of small GTPase mediated signal transduction / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / negative regulation of macrophage derived foam cell differentiation / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / negative regulation of lipid storage / integrin complex / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / cell adhesion mediated by integrin / skin development / microvillus membrane / negative chemotaxis / Syndecan interactions / lung alveolus development / cell-substrate adhesion / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / fibronectin binding / positive regulation of cell adhesion / ECM proteoglycans / voltage-gated calcium channel activity / vasculogenesis / Integrin cell surface interactions / coreceptor activity / specific granule membrane / extrinsic apoptotic signaling pathway in absence of ligand / Signal transduction by L1 / phagocytic vesicle / ERK1 and ERK2 cascade / ribonucleoside triphosphate phosphatase activity / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / T=pseudo3 icosahedral viral capsid / molecular function activator activity / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / cellular response to ionizing radiation / protein kinase C binding / calcium ion transmembrane transport / host cell cytoplasmic vesicle membrane / cell-cell adhesion / ruffle membrane / wound healing / response to virus / bone development / cytoplasmic vesicle membrane / cell morphogenesis / VEGFA-VEGFR2 Pathway / integrin binding / cell junction / viral capsid / virus receptor activity / cell migration / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / clathrin-dependent endocytosis of virus by host cell / receptor complex Similarity search - Function | ||||||||||||
Biological species | Foot-and-mouth disease virus / Homo sapiens (human) / Foot-and-mouth disease virus - type O | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.8 Å | ||||||||||||
Authors | Kotecha A / Stuart D | ||||||||||||
Funding support | United Kingdom, 3 items
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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_3632.map.gz | 7.3 MB | EMDB map data format | |
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Header (meta data) | emd-3632-v30.xml emd-3632.xml | 24.8 KB 24.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3632_fsc.xml | 4.5 KB | Display | FSC data file |
Images | emd_3632.png | 90.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3632 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3632 | HTTPS FTP |
-Validation report
Summary document | emd_3632_validation.pdf.gz | 251.9 KB | Display | EMDB validaton report |
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Full document | emd_3632_full_validation.pdf.gz | 251 KB | Display | |
Data in XML | emd_3632_validation.xml.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3632 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3632 | HTTPS FTP |
-Related structure data
Related structure data | 5nemMC 3630C 3631C 3633C 3634C 3635C 5ne4C 5nedC 5nejC 5nerC 5netC 5neuC 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_3632.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Localised reconstruction of alpha v beta 6 bound to FMDV O PanAsia - Pose A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 virus and Integrin
+Supramolecule #1: Foot and mouth virus and Integrin
+Supramolecule #2: Foot-and-mouth disease virus
+Supramolecule #3: Integrin
+Macromolecule #1: O PanAsia VP1
+Macromolecule #2: O PanAsia VP2
+Macromolecule #3: O PanAsia VP3
+Macromolecule #4: O PanAsia VP4
+Macromolecule #5: Integrin alpha-V
+Macromolecule #6: Integrin beta-6
+Macromolecule #11: alpha-D-mannopyranose
+Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #13: 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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Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Energy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
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 |
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 FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 160000 |
Sample stage | Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |
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-5nem: |