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- EMDB-34496: The core region map of avian influenza A polymerase. -

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Basic information

Entry
Database: EMDB / ID: EMD-34496
TitleThe core region map of avian influenza A polymerase.
Map dataThe core region map of avian influenza A polymerase.
Sample
  • Complex: Influenza A virus RdRp complex
KeywordsPolymerase / VIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi H / Wu Y / Liang H / Liu Y
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530015 China
National Natural Science Foundation of China (NSFC)31870739 China
National Natural Science Foundation of China (NSFC)82071346 China
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: An intermediate state allows influenza polymerase to switch smoothly between transcription and replication cycles.
Authors: Huanhuan Li / Yixi Wu / Minke Li / Lu Guo / Yaqi Gao / Quan Wang / Jihua Zhang / Zhaohua Lai / Xing Zhang / Lixin Zhu / Ping Lan / Zihe Rao / Yingfang Liu / Huanhuan Liang /
Abstract: Influenza polymerase (FluPol) transcribes viral mRNA at the beginning of the viral life cycle and initiates genome replication after viral protein synthesis. However, it remains poorly understood how ...Influenza polymerase (FluPol) transcribes viral mRNA at the beginning of the viral life cycle and initiates genome replication after viral protein synthesis. However, it remains poorly understood how FluPol switches between its transcription and replication states, especially given that the structural bases of these two functions are fundamentally different. Here we propose a mechanism by which FluPol achieves functional switching between these two states through a previously unstudied conformation, termed an 'intermediate state'. Using cryo-electron microscopy, we obtained a structure of the intermediate state of H5N1 FluPol at 3.7 Å, which is characterized by a blocked cap-binding domain and a contracted core region. Structural analysis results suggest that the intermediate state may allow FluPol to transition smoothly into either the transcription or replication state. Furthermore, we show that the formation of the intermediate state is required for both the transcription and replication activities of FluPol, leading us to conclude that the transcription and replication cycles of FluPol are regulated via this intermediate state.
History
DepositionOct 16, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34496.png

Downloads & links

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Map

FileDownload / File: emd_34496.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe core region map of avian influenza A polymerase.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 256 pix.
= 259.584 Å		1.01 Å/pix.
x 256 pix.
= 259.584 Å		1.01 Å/pix.
x 256 pix.
= 259.584 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0068
Minimum - Maximum-0.108838074 - 0.19950533
Average (Standard dev.)0.0002850082 (±0.0044093677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 259.584 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half1 map of core region of avian influenza A polymerase.

Fileemd_34496_half_map_1.map
AnnotationThe half1 map of core region of avian influenza A polymerase.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half2 map of core region of avian influenza A polymerase.

Fileemd_34496_half_map_2.map
AnnotationThe half2 map of core region of avian influenza A polymerase.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza A virus RdRp complex

EntireName: Influenza A virus RdRp complex
Components
  • Complex: Influenza A virus RdRp complex

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Supramolecule #1: Influenza A virus RdRp complex

SupramoleculeName: Influenza A virus RdRp complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 8.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 779360
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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