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- EMDB-66772: Cryo-EM map of influenza polymerase bound to the cRNA promoter -

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Basic information

Entry
Database: EMDB / ID: EMD-66772
TitleCryo-EM map of influenza polymerase bound to the cRNA promoter
Map dataEM map
Sample
  • Complex: influenza polymerase consisting of PA, PB1 and PB2 subunits
Keywordsinfluenza polymerase / VIRAL PROTEIN
Function / homology
Function and homology information


host cell cytosol / cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting ...host cell cytosol / cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / hydrolase activity / nucleotide binding / RNA-directed RNA polymerase activity / host cell nucleus / DNA-templated transcription / RNA binding / metal ion binding / identical protein binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 CAP binding domain ...Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
PB2-S1 / Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesInsecta environmental sample (insect)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWu YX / Liang HH
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82373883 China
CitationJournal: Commun Biol / Year: 2025
Title: Cryo-EM structure of influenza polymerase bound to the cRNA promoter provides insights into the mechanism of viral replication.
Authors: Yixi Wu / Minke Li / Huanhuan Li / Yifan Bai / Tianli Sun / Shaohui Huang / Yingfang Liu / Huanhuan Liang /
Abstract: Influenza virus polymerase (FluPol) synthesizes the complementary RNA (cRNA) and the viral RNA (vRNA) using distinct de novo initiation strategies during genome replication, known as internal and ...Influenza virus polymerase (FluPol) synthesizes the complementary RNA (cRNA) and the viral RNA (vRNA) using distinct de novo initiation strategies during genome replication, known as internal and terminal initiation, respectively. The de novo initiation mechanisms, especially the internal initiation process, which includes a template realignment process, are still not well understood. Here, we present a cryo-electron microscopy structure of H5N1 FluPol bound to the cRNA promoter. In combination with structural analyses and structure-guided mutagenesis studies, we identified several previously unreported structural features of FluPol essential for internal initiation. The B loop adopts an "open" conformation, allowing translocation of the 3' terminus of cRNA (3'-cRNA) template into the catalytic cavity. The dynamic of incoming 3'-cRNA template is limited by the priming and realignment loop (PR loop), which facilitates the cRNA template realignment process. An asparagine cluster above the catalytic cavity is required for polymerase activity. Our findings provide structural insights into the mechanism of replication internal initiation of FluPol.
History
DepositionOct 27, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66772.png

Downloads & links

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Map

FileDownload / File: emd_66772.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
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: 0.005
Minimum - Maximum-0.090534285 - 0.19006704
Average (Standard dev.)0.0001405226 (±0.003182775)
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: EM half2 map

Fileemd_66772_half_map_1.map
AnnotationEM half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM halfl map

Fileemd_66772_half_map_2.map
AnnotationEM halfl map
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 polymerase consisting of PA, PB1 and PB2 subunits

EntireName: influenza polymerase consisting of PA, PB1 and PB2 subunits
Components
  • Complex: influenza polymerase consisting of PA, PB1 and PB2 subunits

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Supramolecule #1: influenza polymerase consisting of PA, PB1 and PB2 subunits

SupramoleculeName: influenza polymerase consisting of PA, PB1 and PB2 subunits
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Insecta environmental sample (insect)

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

34496

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 45973
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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