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- EMDB-5475: Cryo-EM reconstruction of Coxsackievirus B3 strain RD complexed w... -

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Basic information

Entry
Database: EMDB / ID: EMD-5475
TitleCryo-EM reconstruction of Coxsackievirus B3 strain RD complexed with receptor DAF
Map dataCryo-electron microscopy reconstruction of Coxsackievirus B3 strain RD complexed with decay accelerating factor SCR1-4
Sample
  • Sample: Coxsackievirus B3 strain RD (CVB3-RD), complexed with decay-accelerating factor (DAF)
  • Virus: Human coxsackievirus B3
  • Protein or peptide: decay-accelerating factor
Keywordscoxsackievirus / enterovirus / picornavirus / receptor / DAF
Function / homology
Function and homology information


negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / 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) / ficolin-1-rich granule membrane / side of membrane ...negative regulation of complement activation / regulation of lipopolysaccharide-mediated signaling pathway / 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) / ficolin-1-rich granule membrane / side of membrane / COPI-mediated anterograde transport / complement activation, classical pathway / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / Regulation of Complement cascade / positive regulation of T cell cytokine production / virus receptor activity / positive regulation of cytosolic calcium ion concentration / membrane raft / Golgi membrane / innate immune response / lipid binding / Neutrophil degranulation / cell surface / extracellular exosome / extracellular region / plasma membrane
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/SCR/CCP superfamily / Sushi/CCP/SCR domain profile.
Similarity search - Domain/homology
Complement decay-accelerating factor
Similarity search - Component
Biological speciesHomo sapiens (human) / Human coxsackievirus B3
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsYoder JD / Cifuente JO / Pan J / Bergelson JM / Hafenstein S
CitationJournal: J Virol / Year: 2012
Title: The crystal structure of a coxsackievirus B3-RD variant and a refined 9-angstrom cryo-electron microscopy reconstruction of the virus complexed with decay-accelerating factor (DAF) provide a ...Title: The crystal structure of a coxsackievirus B3-RD variant and a refined 9-angstrom cryo-electron microscopy reconstruction of the virus complexed with decay-accelerating factor (DAF) provide a new footprint of DAF on the virus surface.
Authors: Joshua D Yoder / Javier O Cifuente / Jieyan Pan / Jeffrey M Bergelson / Susan Hafenstein /
Abstract: The coxsackievirus-adenovirus receptor (CAR) and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). The first described DAF-binding isolate was ...The coxsackievirus-adenovirus receptor (CAR) and decay-accelerating factor (DAF) have been identified as cellular receptors for coxsackievirus B3 (CVB3). The first described DAF-binding isolate was obtained during passage of the prototype strain, Nancy, on rhabdomyosarcoma (RD) cells, which express DAF but very little CAR. Here, the structure of the resulting variant, CVB3-RD, has been solved by X-ray crystallography to 2.74 Å, and a cryo-electron microscopy reconstruction of CVB3-RD complexed with DAF has been refined to 9.0 Å. This new high-resolution structure permits us to correct an error in our previous view of DAF-virus interactions, providing a new footprint of DAF that bridges two adjacent protomers. The contact sites between the virus and DAF clearly encompass CVB3-RD residues recently shown to be required for binding to DAF; these residues interact with DAF short consensus repeat 2 (SCR2), which is known to be essential for virus binding. Based on the new structure, the mode of the DAF interaction with CVB3 differs significantly from the mode reported previously for DAF binding to echoviruses.
History
DepositionAug 20, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j24
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j24
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5475_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5475.map.gz / Format: CCP4 / Size: 18.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron microscopy reconstruction of Coxsackievirus B3 strain RD complexed with decay accelerating factor SCR1-4
Voxel sizeX=Y=Z: 2.94 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-1.91342664 - 6.09509516
Average (Standard dev.)-0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-85-85-85
Dimensions171171171
Spacing171171171
CellA=B=C: 502.74002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.942.942.94
M x/y/z171171171
origin x/y/z0.0000.0000.000
length x/y/z502.740502.740502.740
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-85-85-85
NC/NR/NS171171171
D min/max/mean-1.9136.095-0.000

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Supplemental data

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Sample components

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Entire : Coxsackievirus B3 strain RD (CVB3-RD), complexed with decay-accel...

EntireName: Coxsackievirus B3 strain RD (CVB3-RD), complexed with decay-accelerating factor (DAF)
Components
  • Sample: Coxsackievirus B3 strain RD (CVB3-RD), complexed with decay-accelerating factor (DAF)
  • Virus: Human coxsackievirus B3
  • Protein or peptide: decay-accelerating factor

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Supramolecule #1000: Coxsackievirus B3 strain RD (CVB3-RD), complexed with decay-accel...

SupramoleculeName: Coxsackievirus B3 strain RD (CVB3-RD), complexed with decay-accelerating factor (DAF)
type: sample / ID: 1000
Details: One DAF binds each binding site (one per CVB3-RD protomer).
Oligomeric state: One receptor per virus protomer / Number unique components: 2
Molecular weightTheoretical: 7 MDa

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Supramolecule #1: Human coxsackievirus B3

SupramoleculeName: Human coxsackievirus B3 / type: virus / ID: 1 / NCBI-ID: 12072 / Sci species name: Human coxsackievirus B3 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 7 MDa
Virus shellShell ID: 1 / Diameter: 300 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 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration2.0 mg/mL
BufferpH: 6 / Details: 50mM MES
GridDetails: Quantifoil
VitrificationCryogen name: ETHANE / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Method: Blot before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45000
Sample stageSpecimen holder: Side mounted nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 83 K / Max: 93 K
Alignment procedureLegacy - Astigmatism: Lens astigmatism was corrected at 98,000 times magnification
Legacy - Electron beam tilt params: 0
DateAug 6, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Number real images: 36 / Average electron dose: 24 e/Å2 / Details: scanned at 7 microns and bin-averaged to 14 / Od range: 1 / Bits/pixel: 8

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Image processing

CTF correctionDetails: AUTO3DEM
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM, CTFFIND, autopp, Robem / Number images used: 3010
DetailsUsing the program Robem, particles were picked from 36 of the highest quality micrographs with a selection area sized to 171x171 pixels and preprocessed using program autopp to remove blemishes, linearize, normalize, and apodize. To correct for contrast transfer function, defocus and astigmatism values were assessed from the digitized images using the program ctffind3.

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Atomic model buiding 1

Initial modelPDB ID:

1ojw


Chain - Chain ID: B
SoftwareName: Chimera
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: average map value
Output model

PDB-3j24:
CryoEM reconstruction of complement decay-accelerating factor

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