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- PDB-8yxr: Structure of Phosphoprotein Tetramer from mumps virus -

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Basic information

Entry
Database: PDB / ID: 8yxr
TitleStructure of Phosphoprotein Tetramer from mumps virus
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Mumps virus polymerase complex / RNA-dependent RNA synthesis / Large protein / phosphoprotein.
Function / homologyP/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Phosphoprotein
Function and homology information
Biological speciesMumps orthorubulavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsLi, T.H. / Shen, Q.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2024
Title: Structures of the mumps virus polymerase complex via cryo-electron microscopy.
Authors: Tianhao Li / Mingdong Liu / Zhanxi Gu / Xin Su / Yunhui Liu / Jinzhong Lin / Yu Zhang / Qing-Tao Shen /
Abstract: The viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), ...The viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), while structures corresponding to these activities remain obscure. Here, we resolved two L-P complex conformations from the mumps virus (MuV), a typical member of nsNSVs, via cryogenic-electron microscopy. One conformation presents all five domains of L forming a continuous RNA tunnel to the methyltransferase domain (MTase), preferably as a transcription state. The other conformation has the appendage averaged out, which is inaccessible to MTase. In both conformations, parallel P tetramers are revealed around MuV L, which, together with structures of other nsNSVs, demonstrates the diverse origins of the L-binding X domain of P. Our study links varying structures of nsNSV polymerase complexes with genome replication and transcription and points to a sliding model for polymerase complexes to advance along the RNA templates.
History
DepositionApr 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details / Item: _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Phosphoprotein
C: Phosphoprotein
D: Phosphoprotein
E: Phosphoprotein


Theoretical massNumber of molelcules
Total (without water)166,6044
Polymers166,6044
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
Phosphoprotein


Mass: 41651.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps orthorubulavirus / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0JJ97
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: tetrameric phosphoproteins from mumps virue / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mumps orthorubulavirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 1/2 BIT CUT-OFF / Num. of particles: 41168 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0051967
ELECTRON MICROSCOPYf_angle_d1.1922645
ELECTRON MICROSCOPYf_dihedral_angle_d4.78264
ELECTRON MICROSCOPYf_chiral_restr0.057334
ELECTRON MICROSCOPYf_plane_restr0.005335

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