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Yorodumi- PDB-5nem: Localised reconstruction of alpha v beta 6 bound to Foot and Mout... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nem | ||||||||||||
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Title | Localised reconstruction of alpha v beta 6 bound to Foot and Mouth Disease Virus O PanAsia - Pose A. | ||||||||||||
Components |
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Keywords | VIRUS / Foot and Mouth Disease Virus / FMDV / OpanAsia / virus-receptor / complex | ||||||||||||
Function / homology | Function and homology information icosahedral viral capsid / Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 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-beta8 complex / integrin alphav-beta6 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 / enamel mineralization / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / symbiont-mediated perturbation of host chromatin organization / bronchiole development / Laminin interactions / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / negative regulation of low-density lipoprotein receptor activity / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / regulation of phagocytosis / phospholipid homeostasis / negative regulation of lipid transport / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / entry into host cell by a symbiont-containing vacuole / surfactant homeostasis / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of intracellular signal transduction / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / microvillus membrane / cell adhesion mediated by integrin / skin development / lung alveolus development / negative chemotaxis / Syndecan interactions / cell-substrate adhesion / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / voltage-gated calcium channel activity / Integrin cell surface interactions / vasculogenesis / specific granule membrane / phagocytic vesicle / coreceptor activity / extrinsic apoptotic signaling pathway in absence of ligand / bone development / ERK1 and ERK2 cascade / positive regulation of cell adhesion / cell-matrix adhesion / ribonucleoside triphosphate phosphatase activity / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / T=pseudo3 icosahedral viral capsid / Signal transduction by L1 / molecular function activator activity / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / cellular response to ionizing radiation / calcium ion transmembrane transport / protein kinase C binding / host cell cytoplasmic vesicle membrane / wound healing / cytoplasmic vesicle membrane / response to virus / cell morphogenesis / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / channel activity / cell migration / integrin binding / cell junction / viral capsid / monoatomic ion transmembrane transport / regulation of translation / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / clathrin-dependent endocytosis of virus by host cell / angiogenesis / host cell cytoplasm / RNA helicase activity / receptor complex Similarity search - Function | ||||||||||||
Biological species | Foot-and-mouth disease virus - type O Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.8 Å | ||||||||||||
Authors | Kotecha, A. / Stuart, D. | ||||||||||||
Funding support | United Kingdom, 3items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5nem.cif.gz | 361.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nem.ent.gz | 283.5 KB | Display | PDB format |
PDBx/mmJSON format | 5nem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nem_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5nem_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5nem_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 5nem_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5nem ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5nem | HTTPS FTP |
-Related structure data
Related structure data | 3632MC 3630C 3631C 3633C 3634C 3635C 5ne4C 5nedC 5nejC 5nerC 5netC 5neuC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Protein , 6 types, 6 molecules 1234AB
#1: Protein | Mass: 23241.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type O / Cell line (production host): BHK 21 / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: A0A1B0SZV3, UniProt: Q98W00*PLUS |
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#2: Protein | Mass: 23914.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type O / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: A0A1B0SZV3, UniProt: Q6ZZ87*PLUS |
#3: Protein | Mass: 23938.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type O / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: J3T9N5, UniProt: Q6ZZ87*PLUS |
#4: Protein | Mass: 7522.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Foot-and-mouth disease virus - type O / Production host: Cricetinae gen. sp. (mammal) / References: UniProt: A6Y878 |
#5: Protein | Mass: 64937.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P06756 |
#6: Protein | Mass: 51534.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB6 / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P18564 |
-Sugars , 6 types, 11 molecules
#7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose | #9: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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: Polysaccharide | alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-alpha-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 #11: Sugar | #12: Sugar | |
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-Non-polymers , 1 types, 4 molecules
#13: Chemical | ChemComp-CA / |
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-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Value: 9 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Details of virus | Empty: NO / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION | ||||||||||||||||||||||||
Natural host | Organism: Bos taurus | ||||||||||||||||||||||||
Virus shell | Name: Foot and Mouth Disease virus / Diameter: 300 nm / Triangulation number (T number): 3 | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Buffer component | Conc.: 50 mM / Name: HEPES | ||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 294 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER Temperature (max): 70 K / Temperature (min): 70 K |
Image recording | Average exposure time: 5 sec. / Electron dose: 18 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 360 |
EM imaging optics | Energyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 2-20 |
-Processing
Software | Name: PHENIX / Version: dev_2283: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 10.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13483 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 120 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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