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- PDB-8sny: Cryo-EM structure of the respiratory syncytial virus polymerase (... -

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Basic information

Entry
Database: PDB / ID: 8sny
TitleCryo-EM structure of the respiratory syncytial virus polymerase (L:P) bound to the trailer complementary promoter
Components
  • Phosphoprotein
  • RNA (5'-R(*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN/RNA / Respiratory syncytial virus / RNA-dependent RNA polymerase / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / NNS virus cap methyltransferase / Translation of respiratory syncytial virus mRNAs / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry ...Respiratory syncytial virus genome transcription / NNS virus cap methyltransferase / Translation of respiratory syncytial virus mRNAs / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Respiratory syncytial virus genome replication / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / ATP binding / metal ion binding
Similarity search - Function
Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V ...Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / RNA-directed RNA polymerase, paramyxovirus / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile. / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirales mRNA-capping domain V / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA / Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesRespiratory syncytial virus A2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsCao, D. / Gao, Y. / Chen, Z. / Gooneratne, I. / Roesler, C. / Mera, C. / Liang, B.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130950 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116788 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129539 United States
Simons FoundationSF349247 United States
CitationJournal: Nature / Year: 2024
Title: Structures of the promoter-bound respiratory syncytial virus polymerase.
Authors: Dongdong Cao / Yunrong Gao / Zhenhang Chen / Inesh Gooneratne / Claire Roesler / Cristopher Mera / Paul D'Cunha / Anna Antonova / Deepak Katta / Sarah Romanelli / Qi Wang / Samantha Rice / ...Authors: Dongdong Cao / Yunrong Gao / Zhenhang Chen / Inesh Gooneratne / Claire Roesler / Cristopher Mera / Paul D'Cunha / Anna Antonova / Deepak Katta / Sarah Romanelli / Qi Wang / Samantha Rice / Wesley Lemons / Anita Ramanathan / Bo Liang /
Abstract: The respiratory syncytial virus (RSV) polymerase is a multifunctional RNA-dependent RNA polymerase composed of the large (L) protein and the phosphoprotein (P). It transcribes the RNA genome into ten ...The respiratory syncytial virus (RSV) polymerase is a multifunctional RNA-dependent RNA polymerase composed of the large (L) protein and the phosphoprotein (P). It transcribes the RNA genome into ten viral mRNAs and replicates full-length viral genomic and antigenomic RNAs. The RSV polymerase initiates RNA synthesis by binding to the conserved 3'-terminal RNA promoters of the genome or antigenome. However, the lack of a structure of the RSV polymerase bound to the RNA promoter has impeded the mechanistic understanding of RSV RNA synthesis. Here we report cryogenic electron microscopy structures of the RSV polymerase bound to its genomic and antigenomic viral RNA promoters, representing two of the first structures of an RNA-dependent RNA polymerase in complex with its RNA promoters in non-segmented negative-sense RNA viruses. The overall structures of the promoter-bound RSV polymerases are similar to that of the unbound (apo) polymerase. Our structures illustrate the interactions between the RSV polymerase and the RNA promoters and provide the structural basis for the initiation of RNA synthesis at positions 1 and 3 of the RSV promoters. These structures offer a deeper understanding of the pre-initiation state of the RSV polymerase and could aid in antiviral research against RSV.
History
DepositionApr 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 20, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
T: RNA (5'-R(*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')


Theoretical massNumber of molelcules
Total (without water)362,4226
Polymers362,4226
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 250704.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28887, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, NNS virus cap methyltransferase
#2: Protein
Phosphoprotein


Mass: 27165.838 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G3C7Q7
#3: RNA chain RNA (5'-R(*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')


Mass: 3053.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Respiratory syncytial virus A2
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: The respiratory syncytial virus polymerase (L:P) bound to the trailer complementary promoter
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Respiratory syncytial virus A2
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 0.35 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 56.86 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197859 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414048
ELECTRON MICROSCOPYf_angle_d0.60919016
ELECTRON MICROSCOPYf_dihedral_angle_d14.5165350
ELECTRON MICROSCOPYf_chiral_restr0.0422207
ELECTRON MICROSCOPYf_plane_restr0.0042372

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