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- PDB-9lck: Cryo-EM structure of influenza polymerase bound to cRNA promoter -

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Basic information

Entry
Database: PDB / ID: 9lck
TitleCryo-EM structure of influenza polymerase bound to cRNA promoter
Components
  • 3'-cRNA
  • 5'-cRNA
  • PB2-S1
  • Polymerase acidic protein
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN/RNA / influenza polymerase / VIRAL PROTEIN-RNA complex
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 / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / 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
RNA / RNA (> 10) / PB2-S1 / Polymerase acidic protein / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesInfluenza A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWu, Y.X. / Liang, H.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM map of influenza polymerase bound to cRNA promoter
Authors: Wu, Y.X.
History
DepositionJan 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: 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
B: RNA-directed RNA polymerase catalytic subunit
C: PB2-S1
D: 3'-cRNA
E: 5'-cRNA


Theoretical massNumber of molelcules
Total (without water)182,7845
Polymers182,7845
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 82669.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)
Gene: PA
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9Q0U9, 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: 86492.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)
Gene: PB1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9Q0V0, RNA-directed RNA polymerase
#3: Protein/peptide PB2-S1 / Polymerase PB2


Mass: 5009.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)
Gene: PB2
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: P0DOG5
#4: RNA chain 3'-cRNA


Mass: 2775.719 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)
#5: RNA chain 5'-cRNA


Mass: 5836.540 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)
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: influenza polymerase / Type: COMPLEX / Entity ID: #1-#2, #4-#5, #3 / Source: RECOMBINANT
Source (natural)Organism: Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)
Source (recombinant)Organism: Insect cell expression vector pTIE1 (others)
Buffer solutionpH: 7.8
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144735 / Symmetry type: POINT
RefinementHighest resolution: 2.98 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410192
ELECTRON MICROSCOPYf_angle_d0.72713883
ELECTRON MICROSCOPYf_dihedral_angle_d8.0531581
ELECTRON MICROSCOPYf_chiral_restr0.0411538
ELECTRON MICROSCOPYf_plane_restr0.0051688

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