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- EMDB-1182: Structural and functional insights into the interaction of echovi... -

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Basic information

Entry
Database: EMDB / ID: EMD-1182
TitleStructural and functional insights into the interaction of echoviruses and decay-accelerating factor.
Map data
SampleEchovirus type 12 bound to decay accelerating factor
  • virus
  • Decay accelerating factor short consensus repeat domains one to four
Function / homology
Function and homology information


regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of complement-dependent cytotoxicity / positive regulation of CD4-positive, alpha-beta T cell activation / Class B/2 (Secretin family receptors) / suppression by virus of host translation initiation factor activity / ficolin-1-rich granule membrane / suppression by virus of host RIG-I activity ...regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of complement activation / respiratory burst / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of complement-dependent cytotoxicity / positive regulation of CD4-positive, alpha-beta T cell activation / Class B/2 (Secretin family receptors) / suppression by virus of host translation initiation factor activity / ficolin-1-rich granule membrane / suppression by virus of host RIG-I activity / COPI-mediated anterograde transport / transport vesicle / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / endoplasmic reticulum-Golgi intermediate compartment membrane / anchored component of membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / secretory granule membrane / RNA-protein covalent cross-linking / complement activation, classical pathway / regulation of complement activation / Regulation of Complement cascade / positive regulation of T cell cytokine production / positive stranded viral RNA replication / integral to membrane of host cell / pore formation by virus in membrane of host cell / virus receptor activity / protein complex oligomerization / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of cytosolic calcium ion concentration / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / suppression by virus of host gene expression / ion channel activity / induction by virus of host autophagy / DNA replication / lipid binding / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / virion attachment to host cell / Golgi membrane / membrane raft / host cell nucleus / innate immune response / Neutrophil degranulation / neutrophil degranulation / structural molecule activity / cell surface / RNA binding / extracellular exosome / membrane / extracellular region / ATP binding / plasma membrane / metal ion binding
Similarity search - Function
Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Picornavirus core protein 2A ...Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain / Peptidase C3, picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Picornavirus coat protein VP4 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Picornavirus capsid / 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 / 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 / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Complement decay-accelerating factor / Genome polyprotein
Similarity search - Component
Biological speciesHuman echovirus 12 (EV12) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 16 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-
UpdateJun 29, 2016-
Current statusJun 29, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2c8i
  • Surface level: 10
  • 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

Downloads & links

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Map

FileDownload / File: emd_1182.map.gz / Format: CCP4 / Size: 61.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelPrimary: 143.0 / Movie #1: 10
Minimum - Maximum-335.404999999999973 - 422.509999999999991
Average (Standard dev.)6.76727 (±60.976199999999999)
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
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS255255255
D min/max/mean-335.405422.5106.767

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Supplemental data

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Sample components

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Entire Echovirus type 12 bound to decay accelerating factor

EntireName: Echovirus type 12 bound to decay accelerating factor / Oligomeric State: Sixty DAF molecules binds to one virion. / Number of components: 2

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Component #1: virus, Human echovirus 12

VirusName: Human echovirus 12 / a.k.a: EV12 / Class: VIRION / Enveloped: No / Empty: No / Isolate: SEROTYPE
SpeciesSpecies: Human echovirus 12 (EV12)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: VP1-4 / Diameter: 300 Å / T number (triangulation number): 3

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Component #2: cellular-component, Decay accelerating factor short consensus rep...

Cellular-componentName: Decay accelerating factor short consensus repeat domains one to four
a.k.a: DAF / Oligomeric Details: Monomer / Number of Copies: 60 / Recombinant expression: Yes
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Komagataella pastoris (fungus)
Source (natural)Location in cell: plasma membrane

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: negative staining, cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / Buffer solution: Phosphate buffered saline / pH: 7.4
Support film400 mesh R2/2 quantifoils
Staining5 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.
VitrificationCryogen name: ETHANE / Method: Blot for two seconds, wait for two seconds.

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Electron microscopy imaging

ImagingMicroscope: JEOL 1200 / Date: Aug 31, 2004
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 30000 X (nominal), 29100 X (calibrated)
Astigmatism: Objective astigmatism corrected at 200,000 times mag
Cs: 3.4 mm / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2800 nm
Specimen HolderHolder: Side entry liquid-nitrogen cooled / Model: OTHER / Temperature: 100
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 192 / Scanner: NIKON COOLSCAN / Sampling size: 6.35 µm / Bit depth: 16 / Details: Scanned on Nikon Coolscan

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 1339 / Applied symmetry: I (正20面体型対称)
3D reconstructionAlgorithm: Orientation and origins determined by Polar Fourier Transform method
Software: PFT2, EM3DR2 / CTF correction: defocus pairs, each particle - CTFmix / Resolution: 16 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Target criteria: correlation coefficient / Refinement space: REAL
Details: Protocol: search using known inter-domain orientations. based on earlier EV12/DAF34 fits using known inter-domain angles from the DAF1234 crystal structures.
Input PDB model: 2C8I
Chain ID: E

Overall bvalue: 95
Output model

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