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Yorodumi- EMDB-5957: Single particle EM reveals plasticity of interactions between the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5957 | |||||||||
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Title | Single particle EM reveals plasticity of interactions between the adenovirus penton base and integrin alphaV-beta3 | |||||||||
Map data | Reconstruction of unliganded integrin | |||||||||
Sample |
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Keywords | adenovirus / integrin / virus infection / electron microscopy / fluorescence correlation microscopy | |||||||||
Function / homology | Function and homology information integrin alphav-beta8 complex / integrin alphav-beta6 complex / 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 ...integrin alphav-beta8 complex / integrin alphav-beta6 complex / 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 / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / negative regulation of lipid transport / regulation of phagocytosis / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / 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 / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / cell adhesion mediated by integrin / microvillus membrane / 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 / negative regulation of macrophage derived foam cell differentiation / fibronectin binding / negative regulation of lipid storage / ECM proteoglycans / vasculogenesis / Integrin cell surface interactions / voltage-gated calcium channel activity / specific granule membrane / coreceptor activity / phagocytic vesicle / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / positive regulation of cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / Signal transduction by L1 / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / protein kinase C binding / calcium ion transmembrane transport / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / integrin binding / cell migration / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / cell adhesion / positive regulation of cell migration / symbiont entry into host cell / external side of plasma membrane / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 44.0 Å | |||||||||
Authors | Veesler D / Cupelli K / Burger M / Graber P / Stehle T / Johnson JE | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 Title: Single-particle EM reveals plasticity of interactions between the adenovirus penton base and integrin αVβ3. Authors: David Veesler / Karolina Cupelli / Markus Burger / Peter Gräber / Thilo Stehle / John E Johnson / Abstract: Human adenoviruses are double-stranded DNA viruses responsible for numerous infections, some of which can be fatal. Furthermore, adenoviruses are currently used in clinical trials as vectors for gene ...Human adenoviruses are double-stranded DNA viruses responsible for numerous infections, some of which can be fatal. Furthermore, adenoviruses are currently used in clinical trials as vectors for gene therapy applications. Although initial binding of adenoviruses to host attachment receptors has been extensively characterized, the interactions with the entry receptor (integrins) remain poorly understood at the structural level. We characterized the interactions between the adenovirus 9 penton base subunit and αVβ3 integrin using fluorescence correlation spectroscopy and single-particle electron microscopy to understand the mechanisms underlying virus internalization and infection. Our results indicate that the penton base subunit can bind integrins with high affinity and in several different orientations. These outcomes correlate with the requirement of the pentameric penton base to simultaneously bind several integrins to enable their clustering and promote virus entry into the host cell. | |||||||||
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_5957.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-5957-v30.xml emd-5957.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | 400_5957.gif 80_5957.gif | 20.5 KB 2.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5957 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5957 | HTTPS FTP |
-Validation report
Summary document | emd_5957_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_5957_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_5957_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5957 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5957 | HTTPS FTP |
-Related structure data
Related structure data | 5955C 5956C 5958C 5959C 5960C 5961C 5962C 5963C 5964C 5965C 5966C 5967C 5968C 5969C 5970C 5971C 5972C 5973C C: citing same article (ref.) |
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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_5957.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of unliganded integrin | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.5 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 : Human alphaV-beta3 integrin ectodomain
Entire | Name: Human alphaV-beta3 integrin ectodomain |
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Components |
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-Supramolecule #1000: Human alphaV-beta3 integrin ectodomain
Supramolecule | Name: Human alphaV-beta3 integrin ectodomain / type: sample / ID: 1000 / Oligomeric state: heterodimer / Number unique components: 1 |
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Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: alphaV-beta3 integrin ectodomain
Macromolecule | Name: alphaV-beta3 integrin ectodomain / type: protein_or_peptide / ID: 1 / Details: Second UniProt identifier: P05106 / Number of copies: 1 / Oligomeric state: heterodimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 180 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pFastBacDual |
Sequence | UniProtKB: Integrin alpha-V |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 10 mM Tris, 150 mM NaCl, 2 mM MnCl2 |
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Staining | Type: NEGATIVE / Details: 2% uranyl formate |
Grid | Details: C-flat 2/0.5 grids overlaid with a thin layer of carbon |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Date | Jun 13, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 540 / Average electron dose: 33 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.55 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 85714 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Random conical tilt reconstruction |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 44.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 769 |
Final two d classification | Number classes: 1 |