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- PDB-9pfr: Cryo-EM structure of the respiratory syncytial virus polymerase (... -

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Basic information

Entry
Database: PDB / ID: 9pfr
TitleCryo-EM structure of the respiratory syncytial virus polymerase (L:P) in NTP-bound elongation state
Components
  • Phosphoprotein
  • RNA (5'-R(P*AP*CP*G)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / TRANSFERASE/RNA / Respiratory syncytial virus / RNA-dependent RNA polymerase / nucleotide addition cycle / VIRAL PROTEIN-RNA complex / TRANSFERASE-RNA complex
Function / homology
Function and homology information


Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...Respiratory syncytial virus genome transcription / Translation of respiratory syncytial virus mRNAs / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Respiratory syncytial virus genome replication / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / 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 / 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 ...Phosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / 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
Chem-ZAN / RNA / RNA (> 10) / Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesRespiratory syncytial virus
Respiratory syncytial virus A2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsCao, D. / Chen, Z. / Gao, Y. / Roesler, C. / Gooneratne, I. / 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: Nat Commun / Year: 2026
Title: Orchestrated and dynamic nucleotide addition cycle during respiratory syncytial virus early-stage elongation.
Authors: Dongdong Cao / Zhenhang Chen / Yunrong Gao / Claire Roesler / Inesh Gooneratne / Cristopher Mera / Lisa Zhuang / Julia Slack / Elijah Nudell-Cook / Jenny Vy / Jasmine Berry / Maurice Royal / ...Authors: Dongdong Cao / Zhenhang Chen / Yunrong Gao / Claire Roesler / Inesh Gooneratne / Cristopher Mera / Lisa Zhuang / Julia Slack / Elijah Nudell-Cook / Jenny Vy / Jasmine Berry / Maurice Royal / Masthan Shaik / Ryan Youngs / Bo Liang /
Abstract: The respiratory syncytial virus (RSV) polymerase (L:P complex) is responsible for viral RNA transcription and replication, where nucleotide addition cycles (NACs) are executed repeatedly during ...The respiratory syncytial virus (RSV) polymerase (L:P complex) is responsible for viral RNA transcription and replication, where nucleotide addition cycles (NACs) are executed repeatedly during elongation in both processes. Using cryo-EM, we capture snapshots of RSV polymerase in action during early-stage elongation and in four distinct NAC states: NTP-bound, pre-reaction, pre-translocation, and post-translocation. Strikingly, we observe all five domains of RSV L in NTP-bound and post-translocation states. In contrast, only two domains are visible in pre-reaction and pre-translocation states, similar to previously reported apo or promoter-bound structures. Importantly, these snapshots reveal the synergistic and dynamic interaction networks among key residues and motifs of RSV polymerase, RNA template, product, incoming nucleotide, and metal ions across NAC states. Our findings provide the first comprehensive insights into orchestrated macro-domain rearrangements and micro-motif changes of RSV polymerase during NAC catalysis, facilitating antiviral therapeutics targeting RSV and related nonsegmented negative-sense RNA viruses, including rabies, Nipah, and Ebola.
History
DepositionJul 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)364,4999
Polymers363,9697
Non-polymers5312
Water00
1


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

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Components

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Protein , 2 types, 5 molecules ABCDE

#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 / Strain: 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 / Strain: A2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: G3C7Q7

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RNA chain , 2 types, 2 molecules PT

#3: RNA chain RNA (5'-R(P*AP*CP*G)-3')


Mass: 934.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Respiratory syncytial virus A2
#4: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*CP*UP*CP*GP*U)-3')


Mass: 3666.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Respiratory syncytial virus A2

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ZAN / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of the respiratory syncytial virus polymerase (L:P) in NTP-bound elongation stateCOMPLEX#1-#40MULTIPLE SOURCES
2respiratory syncytial virus polymeraseCOMPLEX#1-#21RECOMBINANT
3RNACOMPLEX#3-#41SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Respiratory syncytial virus A21972429
33Respiratory syncytial virus A21972429
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: TFS 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: 52.81 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
13Coot3D reconstruction
14PHENIX3D reconstruction
15UCSF ChimeraX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21615 / Symmetry type: POINT
RefinementHighest resolution: 3.08 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318921
ELECTRON MICROSCOPYf_angle_d0.60725644
ELECTRON MICROSCOPYf_dihedral_angle_d14.9367137
ELECTRON MICROSCOPYf_chiral_restr0.0422965
ELECTRON MICROSCOPYf_plane_restr0.0043146

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