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- EMDB-5964: Single particle EM reveals plasticity of interactions between the... -
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Basic information
Entry | Database: EMDB / ID: EMD-5964 | |||||||||
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Title | Single particle EM reveals plasticity of interactions between the adenovirus penton base and integrin alphaV-beta3 | |||||||||
![]() | Reconstruction of the human alphaV-beta3 integrin in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit | |||||||||
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![]() | adenovirus / integrin / virus infection / electron microscopy / fluorescence correlation microscopy | |||||||||
Function / homology | ![]() T=25 icosahedral viral capsid / integrin alphav-beta6 complex / integrin alphav-beta8 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 ...T=25 icosahedral viral capsid / integrin alphav-beta6 complex / integrin alphav-beta8 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-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 / regulation of phagocytosis / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / filopodium membrane / extracellular matrix binding / positive regulation of small GTPase mediated signal transduction / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / 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 / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / 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 / phagocytic vesicle / ERK1 and ERK2 cascade / 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 / endocytosis involved in viral entry into host cell / cell-cell adhesion / ruffle membrane / VEGFA-VEGFR2 Pathway / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 50.0 Å | |||||||||
![]() | Veesler D / Cupelli K / Burger M / Graber P / Stehle T / Johnson JE | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.8 KB 10.8 KB | Display Display | ![]() |
Images | ![]() ![]() | 16.5 KB 2.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5955C ![]() 5956C ![]() 5957C ![]() 5958C ![]() 5959C ![]() 5960C ![]() 5961C ![]() 5962C ![]() 5963C ![]() 5965C ![]() 5966C ![]() 5967C ![]() 5968C ![]() 5969C ![]() 5970C ![]() 5971C ![]() 5972C ![]() 5973C C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of the human alphaV-beta3 integrin in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human alphaV-beta3 integrin ectodomain in complex with the monome...
Entire | Name: Human alphaV-beta3 integrin ectodomain in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit |
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Components |
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-Supramolecule #1000: Human alphaV-beta3 integrin ectodomain in complex with the monome...
Supramolecule | Name: Human alphaV-beta3 integrin ectodomain in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit type: sample / ID: 1000 / Oligomeric state: heterotrimer / Number unique components: 2 |
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Molecular weight | Theoretical: 210 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: ![]() |
Molecular weight | Theoretical: 180 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Integrin alpha-V |
-Macromolecule #2: adenovirus 9 penton base
Macromolecule | Name: adenovirus 9 penton base / type: protein_or_peptide / ID: 2 Details: Only the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit is present in the construct used (residues 116 to 360) Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | UniProtKB: Penton base |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | May 30, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 1600 / Average electron dose: 24 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.1 µm / Nominal magnification: 76097 |
Sample stage | Specimen holder model: OTHER |
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Image processing
Details | Random conical tilt reconstruction |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 588 |
Final two d classification | Number classes: 1 |