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- EMDB-39242: FluPol-NS2-1 complex (hexamer) -

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Basic information

Entry
Database: EMDB / ID: EMD-39242
TitleFluPol-NS2-1 complex (hexamer)
Map data
Sample
  • Complex: FluPol-NS2 complex (hexamer)
    • Complex: FluPol
    • Complex: NS2
KeywordsPROTEIN BINDING
Biological speciesInfluenza A virus (A/Aichi/2/1968(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsPeng Q / Sun JQ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871658 China
National Natural Science Foundation of China (NSFC)32192452 China
CitationJournal: EMBO Rep / Year: 2024
Title: NS2 induces an influenza A RNA polymerase hexamer and acts as a transcription to replication switch.
Authors: Junqing Sun / Lu Kuai / Lei Zhang / Yufeng Xie / Yanfang Zhang / Yan Li / Qi Peng / Yuekun Shao / Qiuxian Yang / Wen-Xia Tian / Junhao Zhu / Jianxun Qi / Yi Shi / Tao Deng / George F Gao /
Abstract: Genome transcription and replication of influenza A virus (FluA), catalyzed by viral RNA polymerase (FluAPol), are delicately controlled across the virus life cycle. A switch from transcription to ...Genome transcription and replication of influenza A virus (FluA), catalyzed by viral RNA polymerase (FluAPol), are delicately controlled across the virus life cycle. A switch from transcription to replication occurring at later stage of an infection is critical for progeny virion production and viral non-structural protein NS2 has been implicated in regulating the switch. However, the underlying regulatory mechanisms and the structure of NS2 remained elusive for years. Here, we determine the cryo-EM structure of the FluAPol-NS2 complex at ~3.0 Å resolution. Surprisingly, three domain-swapped NS2 dimers arrange three symmetrical FluPol dimers into a highly ordered barrel-like hexamer. Further structural and functional analyses demonstrate that NS2 binding not only hampers the interaction between FluAPol and the Pol II CTD because of steric conflicts, but also impairs FluAPol transcriptase activity by stalling it in the replicase conformation. Moreover, this is the first visualization of the full-length NS2 structure. Our findings uncover key molecular mechanisms of the FluA transcription-replication switch and have implications for the development of antivirals.
History
DepositionFeb 26, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39242.png

Downloads & links

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Map

FileDownload / File: emd_39242.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 560 pix.
= 498.4 Å		0.89 Å/pix.
x 560 pix.
= 498.4 Å		0.89 Å/pix.
x 560 pix.
= 498.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.114
Minimum - Maximum-0.0020985575 - 1.7022332
Average (Standard dev.)0.0005402615 (±0.016914677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 498.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39242_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39242_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : FluPol-NS2 complex (hexamer)

EntireName: FluPol-NS2 complex (hexamer)
Components
  • Complex: FluPol-NS2 complex (hexamer)
    • Complex: FluPol
    • Complex: NS2

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Supramolecule #1: FluPol-NS2 complex (hexamer)

SupramoleculeName: FluPol-NS2 complex (hexamer) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: FluPol

SupramoleculeName: FluPol / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/Aichi/2/1968(H3N2))

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Supramolecule #3: NS2

SupramoleculeName: NS2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Influenza A virus (A/Aichi/2/1968(H3N2))

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 351243
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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