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- EMDB-5967: Single particle EM reveals plasticity of interactions between the... -

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Entry
Database: EMDB / ID: EMD-5967
TitleSingle particle EM reveals plasticity of interactions between the adenovirus penton base and integrin alphaV-beta3
Map dataReconstruction of the human alphaV-beta3 integrin in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit
Sample
  • Sample: Human alphaV-beta3 integrin ectodomain in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit
  • Protein or peptide: alphaV-beta3 integrin ectodomain
  • Protein or peptide: adenovirus 9 penton base
Keywordsadenovirus / integrin / virus infection / electron microscopy / fluorescence correlation microscopy
Function / homology
Function and homology information


T=25 icosahedral viral capsid / 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 ...T=25 icosahedral viral capsid / 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 / transforming growth factor beta binding / alphav-beta3 integrin-IGF-1-IGF1R complex / 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 / positive regulation of intracellular signal transduction / Molecules associated with elastic fibres / cell adhesion mediated by integrin / negative chemotaxis / microvillus membrane / Syndecan interactions / cell-substrate adhesion / positive regulation of osteoblast proliferation / endodermal cell differentiation / 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 / Integrin cell surface interactions / voltage-gated calcium channel activity / vasculogenesis / 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 / cell-cell adhesion / VEGFA-VEGFR2 Pathway / calcium ion transmembrane transport / ruffle membrane / cell migration / integrin binding / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / cell adhesion / positive regulation of cell migration / endocytosis involved in viral entry into host cell / 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
Adenovirus penton base protein / Adenovirus penton base protein / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...Adenovirus penton base protein / Adenovirus penton base protein / : / Integrin alpha Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal
Similarity search - Domain/homology
Integrin alpha-V / Penton base
Similarity search - Component
Biological speciesHomo sapiens (human) / Human adenovirus 9
Methodsingle particle reconstruction / negative staining / Resolution: 53.0 Å
AuthorsVeesler D / Cupelli K / Burger M / Graber P / Stehle T / Johnson JE
CitationJournal: 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
DepositionMay 19, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseJul 30, 2014-
UpdateJul 30, 2014-
Current statusJul 30, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5967.gif

Downloads & links

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Map

FileDownload / File: emd_5967.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the human alphaV-beta3 integrin in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 128 pix.
= 524.8 Å		4.1 Å/pix.
x 128 pix.
= 524.8 Å		4.1 Å/pix.
x 128 pix.
= 524.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.50413275 - 3.05120754
Average (Standard dev.)-0.00528955 (±0.09954411)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 524.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z524.800524.800524.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-1.5043.051-0.005

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Supplemental data

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Sample components

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Entire : Human alphaV-beta3 integrin ectodomain in complex with the monome...

EntireName: Human alphaV-beta3 integrin ectodomain in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit
Components
  • Sample: Human alphaV-beta3 integrin ectodomain in complex with the monomeric RGD-loop containing insertion domain of the adenovirus 9 penton base subunit
  • Protein or peptide: alphaV-beta3 integrin ectodomain
  • Protein or peptide: adenovirus 9 penton base

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Supramolecule #1000: Human alphaV-beta3 integrin ectodomain in complex with the monome...

SupramoleculeName: 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
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: alphaV-beta3 integrin ectodomain

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 180 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pFastBacDual
SequenceUniProtKB: Integrin alpha-V

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Macromolecule #2: adenovirus 9 penton base

MacromoleculeName: 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
Source (natural)Organism: Human adenovirus 9
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Rosetta 2 (DE3) / Recombinant plasmid: pET15b
SequenceUniProtKB: Penton base

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 10 mM Tris, 150 mM NaCl, 2 mM MnCl2
StainingType: NEGATIVE / Details: 2% uranyl formate
GridDetails: C-flat 2/0.5 grids overlaid with a thin layer of carbon
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
DateMay 30, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 1600 / Average electron dose: 24 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination 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 stageSpecimen holder model: OTHER

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Image processing

DetailsRandom conical tilt reconstruction
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 53.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 515
Final two d classificationNumber classes: 1

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