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- EMDB-4190: A mechanism for the activation of the influenza virus transcriptase -

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Basic information

Entry
Database: EMDB / ID: 4190
TitleA mechanism for the activation of the influenza virus transcriptase
Map dataEM map of influenza C virus RNA dependent RNA polymerase bound to promoter vRNA
SampleInfluenza C virus polymerase bound to promoter vRNA
  • Polymerase acidic protein
  • RNA-directed RNA polymerase catalytic subunit
  • Polymerase basic protein 2
  • (nucleic-acidNucleic acid) x 2
Function / homologyInfluenza RNA-dependent RNA polymerase subunit PA / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PB1 / PA/PA-X superfamily / Polymerase acidic protein / PB2, C-terminal / RNA-directed RNA polymerase, negative-strand RNA virus / Influenza RNA-dependent RNA polymerase subunit PB2 ...Influenza RNA-dependent RNA polymerase subunit PA / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PB1 / PA/PA-X superfamily / Polymerase acidic protein / PB2, C-terminal / RNA-directed RNA polymerase, negative-strand RNA virus / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PB1 / viral transcription / cap snatching / suppression by virus of host RNA polymerase II activity / 7-methylguanosine mRNA capping / virion / RNA-directed RNA polymerase / endonuclease activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm / Hydrolases, Acting on ester bonds / transcription, DNA-templated / host cell nucleus / nucleotide binding / RNA binding / metal ion binding / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Function and homology information
SourceInfluenza B virus / Influenza B virus (B/Memphis/13/2003)
Methodsingle particle reconstruction / cryo EM / 9.8 Å resolution
AuthorsSerna Martin I / Grimes JM
CitationJournal: Mol. Cell / Year: 2018
Title: A Mechanism for the Activation of the Influenza Virus Transcriptase.
Authors: Itziar Serna Martin / Narin Hengrung / Max Renner / Jane Sharps / Mónica Martínez-Alonso / Simonas Masiulis / Jonathan M Grimes / Ervin Fodor
Abstract: Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For ...Influenza virus RNA polymerase (FluPol), a heterotrimer composed of PB1, PB2, and PA subunits (P3 in influenza C), performs both transcription and replication of the viral RNA genome. For transcription, FluPol interacts with the C-terminal domain (CTD) of RNA polymerase II (Pol II), which enables FluPol to snatch capped RNA primers from nascent host RNAs. Here, we describe the co-crystal structure of influenza C virus polymerase (FluPol) bound to a Ser5-phosphorylated CTD (pS-CTD) peptide. The position of the CTD-binding site at the interface of PB1, P3, and the flexible PB2 C-terminal domains suggests that CTD binding stabilizes the transcription-competent conformation of FluPol. In agreement, both cap snatching and capped primer-dependent transcription initiation by FluPol are enhanced in the presence of pS-CTD. Mutations of amino acids in the CTD-binding site reduce viral mRNA synthesis. We propose a model for the activation of the influenza virus transcriptase through its association with pS-CTD of Pol II.
Validation ReportPDB-ID: 6f5o

SummaryFull reportAbout validation report
DateDeposition: Dec 2, 2017 / Header (metadata) release: Jan 17, 2018 / Map release: Jun 27, 2018 / Last update: Jul 4, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6f5o
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4190.map.gz (map file in CCP4 format, 16385 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.35 Å/pix.
= 216. Å
160 pix
1.35 Å/pix.
= 216. Å
160 pix
1.35 Å/pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.0267 (by author), 0.0267 (movie #1):
Minimum - Maximum-0.07689935 - 0.114877686
Average (Standard dev.)0.0012038854 (0.007842474)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin0.0.0.
Limit159.159.159.
Spacing160160160
CellA=B=C: 216.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0770.1150.001

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Supplemental data

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Sample components

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Entire Influenza C virus polymerase bound to promoter vRNA

EntireName: Influenza C virus polymerase bound to promoter vRNA / Number of components: 6

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Component #1: protein, Influenza C virus polymerase bound to promoter vRNA

ProteinName: Influenza C virus polymerase bound to promoter vRNA / Recombinant expression: No
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Polymerase acidic protein

ProteinName: Polymerase acidic protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.232109 kDa
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, RNA-directed RNA polymerase catalytic subunit

ProteinName: RNA-directed RNA polymerase catalytic subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 84.433266 kDa
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #4: protein, Polymerase basic protein 2

ProteinName: Polymerase basic protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 88.028211 kDa
SourceSpecies: Influenza B virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #5: nucleic-acid, 3' promoter vRNA

Nucleic-acidName: 3' promoter vRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAUACCUCUG CUUC
MassTheoretical: 4.321563 kDa
SourceSpecies: Influenza B virus (B/Memphis/13/2003)

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Component #6: nucleic-acid, 5' promoter vRNA

Nucleic-acidName: 5' promoter vRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGUAGUAACA AGAG
MassTheoretical: 4.55782 kDa
SourceSpecies: Influenza B virus (B/Memphis/13/2003)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.09 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 9159
3D reconstructionResolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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