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- EMDB-2208: Negative stained electron microscopy reconstruction of the viral ... -

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Basic information

Entry
Database: EMDB / ID: EMD-2208
TitleNegative stained electron microscopy reconstruction of the viral polymerase of influenza A virus ribonucleoprotein isolated from virions. Conformation 2.
Map dataInflueza virus polymerase. Conformation 2.
Sample
  • Sample: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1). Polymerase end. Conformation 2.
  • Protein or peptide: PB1
  • Protein or peptide: PA
  • Protein or peptide: PB2
  • Protein or peptide: nucleoprotein
  • RNA: RNA
KeywordsInfluenza / RNA polymerase / ribonucleoprotein / nucleoprotein / nucleocapsid / RNA
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 21.7 Å
AuthorsArranz R / Coloma R / Chichon FJ / Conesa JJ / Carrascosa JL / Valpuesta JM / Ortin J / Martin-Benito J
CitationJournal: Science / Year: 2012
Title: The structure of native influenza virion ribonucleoproteins.
Authors: Rocío Arranz / Rocío Coloma / Francisco Javier Chichón / José Javier Conesa / José L Carrascosa / José M Valpuesta / Juan Ortín / Jaime Martín-Benito /
Abstract: The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with ...The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with the polymerase complex and nucleoprotein (NP), forming ribonucleoproteins (RNPs), which are responsible for virus transcription and replication. We describe the structure of native RNPs derived from virions. They show a double-helical conformation in which two NP strands of opposite polarity are associated with each other along the helix. Both strands are connected by a short loop at one end of the particle and interact with the polymerase complex at the other end. This structure will be relevant for unraveling the mechanisms of nuclear import of parental virus RNPs, their transcription and replication, and the encapsidation of progeny RNPs into virions.
History
DepositionSep 19, 2012-
Header (metadata) releaseOct 10, 2012-
Map releaseDec 5, 2012-
UpdateJan 9, 2013-
Current statusJan 9, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2208_image_E...

Downloads & links

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Map

FileDownload / File: emd_2208.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInflueza virus polymerase. Conformation 2.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 64 pix.
= 271.36 Å		4.24 Å/pix.
x 64 pix.
= 271.36 Å		4.24 Å/pix.
x 64 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.018
Minimum - Maximum-0.04665692 - 0.09073374
Average (Standard dev.)-0.00078601 (±0.01224651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.244.244.24
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0470.091-0.001

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Supplemental data

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Sample components

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Entire : Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1...

EntireName: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1). Polymerase end. Conformation 2.
Components
  • Sample: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1). Polymerase end. Conformation 2.
  • Protein or peptide: PB1
  • Protein or peptide: PA
  • Protein or peptide: PB2
  • Protein or peptide: nucleoprotein
  • RNA: RNA

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Supramolecule #1000: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1...

SupramoleculeName: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1). Polymerase end. Conformation 2.
type: sample / ID: 1000 / Number unique components: 5

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Macromolecule #1: PB1

MacromoleculeName: PB1 / type: protein_or_peptide / ID: 1 / Name.synonym: PB1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33 (H1N1)
Molecular weightExperimental: 86 KDa / Theoretical: 86 KDa

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Macromolecule #2: PA

MacromoleculeName: PA / type: protein_or_peptide / ID: 2 / Name.synonym: PA / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33 (H1N1)
Molecular weightExperimental: 83 KDa / Theoretical: 83 KDa

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Macromolecule #3: PB2

MacromoleculeName: PB2 / type: protein_or_peptide / ID: 3 / Name.synonym: PB2 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33 (H1N1)
Molecular weightExperimental: 86 KDa / Theoretical: 86 KDa

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Macromolecule #4: nucleoprotein

MacromoleculeName: nucleoprotein / type: protein_or_peptide / ID: 4 / Name.synonym: nucleoprotein / Recombinant expression: No
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33 (H1N1)
Molecular weightTheoretical: 56 KDa

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Macromolecule #5: RNA

MacromoleculeName: RNA / type: rna / ID: 5 / Name.synonym: RNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Influenza A virus

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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: 8
Details: 50mM Tris-HCl,100mM KCl,5mM MgCl2,0.5% Igepal,150mM imidazole
StainingType: NEGATIVE
Details: Samples were applied to one side of a carbon coated Cu/Rh grid and stained on 2% w/v uranyl acetate for 90 seconds.
GridDetails: Freshly carbon coated, glow discharged for 15 seconds.
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 65000
Sample stageSpecimen holder model: OTHER
DateMay 1, 2011
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1024 / Details: downsampling factor 2. / Bits/pixel: 16
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each plate
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.7 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: XMIPP / Number images used: 8938

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