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- EMDB-5179: The Interaction of Decay-accelerating Factor with Echovirus 7 -

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Basic information

Entry
Database: EMDB / ID: EMD-5179
TitleThe Interaction of Decay-accelerating Factor with Echovirus 7
Map dataCryoEM reconstruction of human echovirus in complex with its cellular receptor DAF. (The map has positive values in regions of protein and nucleic acid density.)
Sample
  • Sample: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)
  • Virus: Human echovirus 7
  • Protein or peptide: Decay Accelerating Factor
KeywordsVIRUS / RECEPTOR / COMPLEX / ECHOVIRUS / DAF / ICOSAHEDRAL VIRUS
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 / transport vesicle / side of membrane / COPI-mediated anterograde transport / 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 / virion component / viral capsid / host cell / nucleoside-triphosphate phosphatase / channel activity / positive regulation of cytosolic calcium ion concentration / virus receptor activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / membrane raft / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / Golgi membrane / symbiont-mediated activation of host autophagy / 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 / symbiont entry into host cell / 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 / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like ...: / 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 / Picornavirus coat protein / 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 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Human echovirus 7
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsPLEVKA P / HAFENSTEIN S / ZHANG Y / HARRIS KG / CIEFUENTE JO / BOWMAN VD / CHIPMAN PR / LIN F / MEDOF DE / BATOR CM / ROSSMANN MG
CitationJournal: J Virol / Year: 2010
Title: Interaction of decay-accelerating factor with echovirus 7.
Authors: Pavel Plevka / Susan Hafenstein / Katherine G Harris / Javier O Cifuente / Ying Zhang / Valorie D Bowman / Paul R Chipman / Carol M Bator / Feng Lin / M Edward Medof / Michael G Rossmann /
Abstract: Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral ...Echovirus 7 (EV7) belongs to the Enterovirus genus within the family Picornaviridae. Many picornaviruses use IgG-like receptors that bind in the viral canyon and are required to initiate viral uncoating during infection. However, in addition, some of the enteroviruses use an alternative or additional receptor that binds outside the canyon. Decay-accelerating factor (DAF) has been identified as a cellular receptor for EV7. The crystal structure of EV7 has been determined to 3.1-Å resolution and used to interpret the 7.2-Å-resolution cryo-electron microscopy reconstruction of EV7 complexed with DAF. Each DAF binding site on EV7 is near a 2-fold icosahedral symmetry axis, which differs from the binding site of DAF on the surface of coxsackievirus B3, indicating that there are independent evolutionary processes by which DAF was selected as a picornavirus accessory receptor. This suggests that there is an advantage for these viruses to recognize DAF during the initial process of infection.
History
DepositionApr 6, 2010-
Header (metadata) releaseNov 17, 2010-
Map releaseNov 17, 2010-
UpdateSep 23, 2011-
Current statusSep 23, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.8
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  • Surface view with fitted model
  • Atomic models: PDB-3iyp
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5179_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5179.map.gz / Format: CCP4 / Size: 19.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of human echovirus in complex with its cellular receptor DAF. (The map has positive values in regions of protein and nucleic acid density.)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.65 Å/pix.
x 173 pix.
= 458.45 Å		2.65 Å/pix.
x 173 pix.
= 458.45 Å		2.65 Å/pix.
x 173 pix.
= 458.45 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8 / Movie #1: 0.8
Minimum - Maximum-2.92487 - 22.099
Average (Standard dev.)1.55084 (±4.00767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-86-86-86
Dimensions173173173
Spacing173173173
CellA=B=C: 458.45 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.652.652.65
M x/y/z173173173
origin x/y/z0.0000.0000.000
length x/y/z458.450458.450458.450
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-86-86-86
NC/NR/NS173173173
D min/max/mean-2.92522.0991.551

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Supplemental data

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Sample components

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Entire : Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)

EntireName: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)
Components
  • Sample: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)
  • Virus: Human echovirus 7
  • Protein or peptide: Decay Accelerating Factor

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Supramolecule #1000: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)

SupramoleculeName: Human Echovirus 7 in complex with Decay-accelerating Factor (DAF)
type: sample / ID: 1000
Oligomeric state: one DAF molecule binds to one asymmetric unit of EV7
Number unique components: 2
Molecular weightTheoretical: 6.8 MDa

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Supramolecule #1: Human echovirus 7

SupramoleculeName: Human echovirus 7 / type: virus / ID: 1 / Name.synonym: human echovirus 7 / NCBI-ID: 46018 / Sci species name: Human echovirus 7 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: human echovirus 7
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 5.2 MDa
Virus shellShell ID: 1 / Diameter: 320 Å / T number (triangulation number): 1

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Macromolecule #1: Decay Accelerating Factor

MacromoleculeName: Decay Accelerating Factor / type: protein_or_peptide / ID: 1 / Name.synonym: DAF / Number of copies: 60 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: Plasma membrane
Molecular weightTheoretical: 26 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus) / Recombinant plasmid: pPICZaA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.2 / Details: 0.1 M NaCl, 20mM Tris
VitrificationCryogen name: ETHANE / Chamber temperature: 113 K / Instrument: OTHER
Timed resolved state: Vitrified 1 hour after mixing DAF with EV7
Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureAverage: 100 K
DetailsMicrographs were digitized with a Zeiss PHODIS microdensitometer at 7-micron intervals.
DateJan 1, 2000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 81 / Average electron dose: 20 e/Å2 / Details: The scans were averaged in boxes of 2x2 pixels.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.67 µm / Nominal defocus min: 1.12 µm
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder.
Specimen holder model: OTHER

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem / Number images used: 11430

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Atomic model buiding 1

Initial modelPDB ID:

2x5i

DetailsEV7 capsid protein coordinates were positioned into the cryoEM reconstruction by superimposing icosahedral symmetry elements.
RefinementSpace: REAL
Output model

PDB-3iyp:
The Interaction of Decay-accelerating Factor with Echovirus 7

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Atomic model buiding 2

Initial modelPDB ID:

1ojy


Chain - Chain ID: a
SoftwareName: EMfit
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Rcrit
Output model

PDB-3iyp:
The Interaction of Decay-accelerating Factor with Echovirus 7

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