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- EMDB-1183: Structural and functional insights into the interaction of echovi... -

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Basic information

Entry
Database: EMDB / ID: EMD-1183
TitleStructural and functional insights into the interaction of echoviruses and decay-accelerating factor.
Map dataReconstruction of Echovirus type 12
Sample
  • Sample: Echovirus type 12
  • Virus: Human echovirus 12
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / regulation of complement-dependent cytotoxicity / regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of CD4-positive, alpha-beta T cell proliferation / Class B/2 (Secretin family receptors) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / ficolin-1-rich granule membrane / complement activation, classical pathway / COPI-mediated anterograde transport / transport vesicle / side of membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / positive regulation of T cell cytokine production / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / virus receptor activity / channel activity / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / membrane raft / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / Golgi membrane / innate immune response / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / Neutrophil degranulation / virion attachment to host cell / host cell nucleus / structural molecule activity / cell surface / ATP hydrolysis activity / proteolysis / RNA binding / extracellular exosome / extracellular region / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
: / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Picornavirus coat protein VP4 superfamily / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein ...: / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Picornavirus coat protein VP4 superfamily / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Complement decay-accelerating factor / Genome polyprotein
Similarity search - Component
Biological speciesHuman echovirus 12
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.0 Å
AuthorsPettigrew DM / Williams DT / Kerrigan D / Evans DJ / Lea SM / Bhella D
CitationJournal: J Biol Chem / Year: 2006
Title: Structural and functional insights into the interaction of echoviruses and decay-accelerating factor.
Authors: David M Pettigrew / David T Williams / David Kerrigan / David J Evans / Susan M Lea / David Bhella /
Abstract: Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo- ...Many enteroviruses bind to the complement control protein decay-accelerating factor (DAF) to facilitate cell entry. We present here a structure for echovirus (EV) type 12 bound to DAF using cryo-negative stain transmission electron microscopy and three-dimensional image reconstruction to 16-A resolution, which we interpreted using the atomic structures of EV11 and DAF. DAF binds to a hypervariable region of the capsid close to the 2-fold symmetry axes in an interaction that involves mostly the short consensus repeat 3 domain of DAF and the capsid protein VP2. A bulge in the density for the short consensus repeat 3 domain suggests that a loop at residues 174-180 rearranges to prevent steric collision between closely packed molecules at the 2-fold symmetry axes. Detailed analysis of receptor interactions between a variety of echoviruses and DAF using surface plasmon resonance and comparison of this structure (and our previous work; Bhella, D., Goodfellow, I. G., Roversi, P., Pettigrew, D., Chaudhry, Y., Evans, D. J., and Lea, S. M. (2004) J. Biol. Chem. 279, 8325-8332) with reconstructions published for EV7 bound to DAF support major differences in receptor recognition among these viruses. However, comparison of the electron density for the two virus.receptor complexes (rather than comparisons of the pseudo-atomic models derived from fitting the coordinates into these densities) suggests that the dramatic differences in interaction affinities/specificities may arise from relatively subtle structural differences rather than from large-scale repositioning of the receptor with respect to the virus surface.
History
DepositionDec 5, 2005-
Header (metadata) releaseDec 5, 2005-
Map releaseDec 5, 2005-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 115.034506112
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 115.034506112
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2c8i
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1183.gif

Downloads & links

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Map

FileDownload / File: emd_1183.map.gz / Format: CCP4 / Size: 61.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Echovirus type 12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 255 pix.
= 555.9 Å		2.18 Å/pix.
x 255 pix.
= 555.9 Å		2.18 Å/pix.
x 255 pix.
= 555.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 148.0 / Movie #1: 115.0345061
Minimum - Maximum-239.683999999999997 - 445.577999999999975
Average (Standard dev.)6.39581 (±58.9574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions255255255
Spacing255255255
CellA=B=C: 555.9 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z255255255
origin x/y/z0.0000.0000.000
length x/y/z555.900555.900555.900
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-96-96
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS255255255
D min/max/mean-239.684445.5786.396

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Supplemental data

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Sample components

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Entire : Echovirus type 12

EntireName: Echovirus type 12
Components
  • Sample: Echovirus type 12
  • Virus: Human echovirus 12

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Supramolecule #1000: Echovirus type 12

SupramoleculeName: Echovirus type 12 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human echovirus 12

SupramoleculeName: Human echovirus 12 / type: virus / ID: 1 / Name.synonym: EV12 / NCBI-ID: 35293 / Sci species name: Human echovirus 12 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: EV12
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: VP1-4 / Diameter: 300 Å / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: Phosphate buffered saline
StainingType: NEGATIVE
Details: 5 microlitres of sample was loaded onto a quantifoil grid and then floated on a 20 microlitre droplet of 15% Ammonium Molybdate for 10 seconds, then the grid was blotted for 2 seconds before ...Details: 5 microlitres of sample was loaded onto a quantifoil grid and then floated on a 20 microlitre droplet of 15% Ammonium Molybdate for 10 seconds, then the grid was blotted for 2 seconds before vitrification in liquid ethane.
GridDetails: 400 mesh R2/2 quantifoils
VitrificationCryogen name: ETHANE / Method: Blot for two seconds, wait for two seconds.

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Electron microscopy

MicroscopeJEOL 1200
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective astigmatism corrected at 200,000 times mag
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 6.35 µm / Number real images: 84 / Details: Scanned on Nikon Coolscan / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 29100 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 30000
Sample stageSpecimen holder: Side entry liquid-nitrogen cooled / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: defocus pairs, each particle - CTFmix
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT2 and EM3DR2 / Number images used: 1501

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