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- EMDB-2209: Organization of the Influenza Virus Replication Machinery -

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Basic information

Entry
Database: EMDB / ID: EMD-2209
TitleOrganization of the Influenza Virus Replication Machinery
Map dataInfluenza RNP Central filament region
Sample
  • Sample: influenza virus ribonucleoprotein complex central filament region
  • Protein or peptide: influenza virus ribonucleoprotein complex
KeywordsInfluenza / RNP / Polymerase
Function / homology
Function and homology information


helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / 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 (A/Puerto Rico/8/1934(H1N1))
Methodhelical reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsMoeller A / Kirchdoerfer RN / Potter CS / Carragher B / Wilson IA
CitationJournal: Science / Year: 2012
Title: Organization of the influenza virus replication machinery.
Authors: Arne Moeller / Robert N Kirchdoerfer / Clinton S Potter / Bridget Carragher / Ian A Wilson /
Abstract: Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies ...Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies of the viral nucleoprotein. In vitro cell expression of all RNP protein components with four of the eight influenza virus gene segments enabled structural determination of native influenza virus RNPs by means of cryogenic electron microscopy (cryo-EM). The cryo-EM structure reveals the architecture and organization of the native RNP, defining the attributes of its largely helical structure and how polymerase interacts with nucleoprotein and the viral genome. Observations of branched-RNP structures in negative-stain electron microscopy and their putative identification as replication intermediates suggest a mechanism for viral replication by a second polymerase on the RNP template.
History
DepositionOct 5, 2012-
Header (metadata) releaseOct 24, 2012-
Map releaseDec 5, 2012-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2ymn
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2209.tif

Downloads & links

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Map

FileDownload / File: emd_2209.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInfluenza RNP Central filament region
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 144 pix.
= 236.16 Å		1.64 Å/pix.
x 144 pix.
= 236.16 Å		1.64 Å/pix.
x 144 pix.
= 236.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065 / Movie #1: 0.0065
Minimum - Maximum-0.00893382 - 0.01736183
Average (Standard dev.)0.00096677 (±0.00387478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-72-72-72
Dimensions144144144
Spacing144144144
CellA=B=C: 236.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z236.160236.160236.160
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.0090.0170.001

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Supplemental data

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Sample components

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Entire : influenza virus ribonucleoprotein complex central filament region

EntireName: influenza virus ribonucleoprotein complex central filament region
Components
  • Sample: influenza virus ribonucleoprotein complex central filament region
  • Protein or peptide: influenza virus ribonucleoprotein complex

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Supramolecule #1000: influenza virus ribonucleoprotein complex central filament region

SupramoleculeName: influenza virus ribonucleoprotein complex central filament region
type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: influenza virus ribonucleoprotein complex

MacromoleculeName: influenza virus ribonucleoprotein complex / type: protein_or_peptide / ID: 1 / Name.synonym: Influenza RNP
Details: Helical assembly of one strand of single stranded RNA bound to several nucleoproteins
Recombinant expression: Yes
Source (natural)Organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TECNAI 20
DateAug 27, 2010
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Number real images: 3437 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF
Software - Name: IHRSR, XMIPP, IMAGIC, SPIDER, APPION, CTFFIND3
CTF correctionDetails: wholeimage

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Atomic model buiding 1

Initial modelPDB ID:

2iqh


Chain - Chain ID: A
SoftwareName: Chimera
RefinementSpace: REAL
Output model

PDB-2ymn:
Organization of the Influenza Virus Replication Machinery

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