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- PDB-9oce: 2.48A cryo-EM structure of the Measles Virus L-P-C in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9oce
Title2.48A cryo-EM structure of the Measles Virus L-P-C in complex with ERdRp-0519
Components
  • Phosphoprotein
  • Protein C
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / TRANSFERASE / Measles virus / L protein / phosphoprotein / RNA-dependent RNA polymerase / PRNTase / GDP polyribonucleotidyl transferase / RNA capping / MTase / viral replication / C protein / ERdRp-0519
Function / homology
Function and homology information


GDP polyribonucleotidyltransferase / host cell cytoplasmic vesicle / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / viral genome replication / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity ...GDP polyribonucleotidyltransferase / host cell cytoplasmic vesicle / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Transferases; Transferring one-carbon groups; Methyltransferases / viral genome replication / virion component / host cell cytoplasm / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTPase activity / DNA-templated transcription / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Paramyxoviridae nonstructural protein C / Non-structural protein C / RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Mononegavirus L protein 2-O-ribose methyltransferase / RNA-directed RNA polymerase L, C-terminal ...Paramyxoviridae nonstructural protein C / Non-structural protein C / RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / RNA-directed RNA polymerase, paramyxovirus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / Protein C / Phosphoprotein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesMeasles virus strain Edmonston-B
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsLiu, B. / Wang, D. / Yang, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 2.48A cryo-EM structure of the Measles Virus L-P-C in complex with ERdRp-0519
Authors: Liu, B. / Wang, D. / Yang, G.
History
DepositionApr 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 3, 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: RNA-directed RNA polymerase L
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein
F: Protein C
G: Protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)506,9268
Polymers506,3977
Non-polymers5301
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 RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 247910.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus strain Edmonston-B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q83626, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, Transferases; Transferring ...References: UniProt: Q83626, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein
Phosphoprotein / Protein P


Mass: 54088.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus strain Edmonston-B / Gene: P/V / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q83623
#3: Protein Protein C


Mass: 21066.365 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus strain Edmonston-B / Gene: C, P / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q783Q9
#4: Chemical ChemComp-A1EF9 / 2-methyl-~{N}-[4-[(2~{S})-2-(2-morpholin-4-ylethyl)piperidin-1-yl]sulfonylphenyl]-5-(trifluoromethyl)pyrazole-3-carboxamide


Mass: 529.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30F3N5O4S / Feature type: SUBJECT OF INVESTIGATION
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

ComponentName: the Measles Virus L-P-C in complex with ERdRp-0519 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.61 MDa / Experimental value: YES
Source (natural)Organism: Measles virus strain Edmonston-B
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
Details: 50 mM Tris-HCl pH 8.0, 250 mM NaCl, 5% glycerol, 1 mM TCEP, and 4 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 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 / Temperature (max): 77 K / Temperature (min): 63 K
Image recordingAverage exposure time: 1.7 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8046
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21_5207:model refinement
3EPUimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4333399
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 524675 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Symmetry type: POINT
Atomic model buildingB value: 75.98 / Protocol: OTHER / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00520806
ELECTRON MICROSCOPYf_angle_d0.85828130
ELECTRON MICROSCOPYf_dihedral_angle_d5.9042777
ELECTRON MICROSCOPYf_chiral_restr0.0533230
ELECTRON MICROSCOPYf_plane_restr0.0093526

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