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- EMDB-2205: Cryo-electron microscopy reconstruction of the helical part of in... -

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Basic information

Entry
Database: EMDB / ID: EMD-2205
TitleCryo-electron microscopy reconstruction of the helical part of influenza A virus ribonucleoprotein isolated from virions.
Map dataReconstruction of the helical part of the influeza A virus ribonucleoprotein
Sample
  • Sample: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1)
  • Protein or peptide: nucleoprotein
  • RNA: RNA
KeywordsInfluenza / ribonucleoprotein / nucleoprotein / nucleocapsid / RNA / helical structure
Function / homology
Function and homology information


negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesInfluenza A virus
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 18.0 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 18, 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: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4bbl
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2205.tif

Downloads & links

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Map

FileDownload / File: emd_2205.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the helical part of the influeza A virus ribonucleoprotein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.42 Å/pix.
x 100 pix.
= 442. Å		4.42 Å/pix.
x 100 pix.
= 442. Å		4.42 Å/pix.
x 100 pix.
= 442. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.02651748 - 0.03940119
Average (Standard dev.)0.0009318 (±0.00564078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 442.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.424.424.42
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z442.000442.000442.000
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/NS100100100
D min/max/mean-0.0270.0390.001

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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)
Components
  • Sample: Native influenza A virus ribonucleoprotein (STRAIN A/WSN/33, H1N1)
  • 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)
type: sample / ID: 1000
Oligomeric state: Helical structure of nucleoprotein bound to single stranded RNA
Number unique components: 2

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Macromolecule #1: nucleoprotein

MacromoleculeName: nucleoprotein / type: protein_or_peptide / ID: 1 / Oligomeric state: helical / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Influenza A virus / Strain: A/WSN/33 (H1N1)
Molecular weightTheoretical: 56 KDa

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Name.synonym: vRNA / 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, cryo EM
Processinghelical 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 Quantifoil holey carbon grid, blotted and plunged into liquid ethane
GridDetails: Freshly carbon coated Quantifoil R 2/2 holey carbon grids.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC / Method: Blot for 2 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: checking CTF.
DateJan 1, 2011
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 559 / Details: downsampling factor = 2. / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 65000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: OTHER / Software - Name: Spider, XMIPP
CTF correctionDetails: Each plate

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Atomic model buiding 1

Initial modelPDB ID:

2iqh


Chain - Chain ID: A
SoftwareName: Chimera, SITUS
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Volumetric
Output model

PDB-4bbl:
Cryo-electron microscopy reconstruction of the helical part of influenza A virus ribonucleoprotein isolated from virions.

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