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- PDB-9rag: Influenza A/H7N9 polymerase in complex with a 70-mer RNA template... -

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Basic information

Entry
Database: PDB / ID: 9rag
TitleInfluenza A/H7N9 polymerase in complex with a 70-mer RNA template, in stalled elongation.
Components
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA Pol II CTD 6 repeats (site 1A/2A)
  • RNA product
  • RNA template (70-mer)
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN / Influenza polymerase
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / hydrolase activity / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / 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-dependent RNA polymerase subunit PB2 / PB2, C-terminal / 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 C-terminal domain / : / Influenza RNA polymerase PB2 6th 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
PYROPHOSPHATE 2- / RNA / RNA (> 10) / Polymerase basic protein 2 / Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsArragain, B. / Cusack, S.
Funding support1items
OrganizationGrant numberCountry
European m
CitationJournal: Science / Year: 2026
Title: Polymerase trapping as mechanism of H5 highly pathogenic avian influenza virus genesis
Authors: Funk, M. / Spronken, M.I. / Hutchinson, R. / Arragain, B. / Juyoux, P. / Bestebroer, T.M. / de Bruin, A.C. / Gultyaev, A.P. / Fouchier, R.A.M. / Cusack, S. / te Vulthuis, A.J.W. / Richard, M.
History
DepositionMay 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
C: Polymerase basic protein 2
G: RNA Pol II CTD 6 repeats (site 1A/2A)
M: RNA product
B: RNA-directed RNA polymerase catalytic subunit
T: RNA template (70-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,39810
Polymers289,1496
Non-polymers2494
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 3 molecules ACB

#1: Protein Polymerase acidic protein


Mass: 82829.578 Da / Num. of mol.: 1 / Mutation: E349K; R490I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Gene: PA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: M9TI86
#2: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 89038.625 Da / Num. of mol.: 1 / Mutation: G74R; K627; D701
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Gene: PB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A024E1J5
#5: Protein RNA-directed RNA polymerase catalytic subunit


Mass: 86424.031 Da / Num. of mol.: 1 / Mutation: K577G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Gene: PB1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: S5ME50

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Protein/peptide , 1 types, 1 molecules G

#3: Protein/peptide RNA Pol II CTD 6 repeats (site 1A/2A)


Mass: 4816.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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RNA chain , 2 types, 2 molecules MT

#4: RNA chain RNA product


Mass: 3560.210 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
#6: RNA chain RNA template (70-mer)


Mass: 22480.326 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

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Non-polymers , 3 types, 671 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Influenza A/H7N9 polymerase in complex with a 70-mer RNA template, in stalled elongation.
Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 41 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
3EPUimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1030984 / Symmetry type: POINT
RefinementHighest resolution: 1.99 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215264
ELECTRON MICROSCOPYf_angle_d0.46320821
ELECTRON MICROSCOPYf_dihedral_angle_d12.8552569
ELECTRON MICROSCOPYf_chiral_restr0.0372301
ELECTRON MICROSCOPYf_plane_restr0.0032519

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