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- PDB-9rve: Structure of human 1918 influenza A polymerase heterotrimer in co... -

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Basic information

Entry
Database: PDB / ID: 9rve
TitleStructure of human 1918 influenza A polymerase heterotrimer in complex with 1918 NEP.
Components
  • Nuclear export protein
  • Polymerase acidic protein
  • Polymerase basic protein 2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN / influenza virus / nuclear export / NEP / NS2 / 1918 polymerase / spanish Flu / viral polymerase / cryo-EM
Function / homology
Function and homology information


exit of virus from host cell nucleus through nuclear pore / 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 ...exit of virus from host cell nucleus through nuclear pore / 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 / 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 nuclear export protein NS2 / Influenza non-structural protein (NS2) / 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 nuclear export protein NS2 / Influenza non-structural protein (NS2) / 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
Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 2 / Nuclear export protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsRep, A. / Wang, F. / Chen, K. / Carrique, L. / Grimes, J.M. / Fodor, M.
Funding support United Kingdom, 8items
OrganizationGrant numberCountry
Wellcome Trust200835/Z/16/Z United Kingdom
Wellcome Trust222510/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R009945/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/X008312/1 United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
Wellcome Trust227570/Z/23/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of human 1918 influenza A polymerase heterotrimer in complex with 1918 NEP.
Authors: Rep, A. / Wang, F. / Chen, K. / Carrique, L. / Grimes, J.M. / Fodor, M.
History
DepositionJul 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase acidic protein
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase basic protein 2
D: Nuclear export protein


Theoretical massNumber of molelcules
Total (without water)271,4514
Polymers271,4514
Non-polymers00
Water00
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

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 82707.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Gene: PA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q3HM39, Hydrolases; Acting on ester bonds
#2: Protein RNA-directed RNA polymerase catalytic subunit / Polymerase basic protein 1 / PB1 / RNA-directed RNA polymerase subunit P1


Mass: 86625.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Gene: PB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3HM40, RNA-directed RNA polymerase
#3: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 86849.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Gene: PB2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3HM41
#4: Protein Nuclear export protein / NEP / Non-structural protein 2 / NS2


Mass: 15269.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GST-3C-NEP fusion protein,GST-3C-NEP fusion protein
Source: (gene. exp.) Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Gene: NS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q77IX1
Has protein modificationN

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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: Structure of human 1918 influenza A polymerase heterotrimer in complex with 1918 NEP
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.283 MDa / Experimental value: YES
Source (natural)Organism: Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
125 mMHEPES1
2150 mMNaCl1
31
SpecimenConc.: 0.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 24000 nm / Nominal defocus min: 5000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2 - 4.7particle selection
2EPU3.14image acquisition
4cryoSPARC4.2 - 4.7CTF correction
7UCSF ChimeraX1.7model fitting
8Coot0.9.8.3model fitting
10cryoSPARC4.2 - 4.7initial Euler assignment
11cryoSPARC4.2 - 4.7final Euler assignment
12cryoSPARC4.2 - 4.7classification
13cryoSPARC4.2 - 4.73D reconstruction
14PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105000 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003114889
ELECTRON MICROSCOPYf_angle_d0.504620055
ELECTRON MICROSCOPYf_chiral_restr0.03752191
ELECTRON MICROSCOPYf_plane_restr0.00372582
ELECTRON MICROSCOPYf_dihedral_angle_d4.19861972

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