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- PDB-7ewq: Structure of Mumps virus nucleocapsid ring -

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Entry
Database: PDB / ID: 7ewq
TitleStructure of Mumps virus nucleocapsid ring
Components
  • Nucleoprotein
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
KeywordsNUCLEAR PROTEIN / nucleocapcid / Mumps virus
Function / homology
Function and homology information


helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesMumps virus
Mumps orthorubulavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSu, X. / Shen, Q. / Shan, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870743 China
CitationJournal: Commun Biol / Year: 2021
Title: Structural plasticity of mumps virus nucleocapsids with cryo-EM structures.
Authors: Hong Shan / Xin Su / Tianhao Li / Yuqi Qin / Na Zhang / Liuyan Yang / Linsha Ma / Yun Bai / Lei Qi / Yunhui Liu / Qing-Tao Shen /
Abstract: Mumps virus (MuV) is a highly contagious human pathogen and frequently causes worldwide outbreaks despite available vaccines. Similar to other mononegaviruses such as Ebola and rabies, MuV uses a ...Mumps virus (MuV) is a highly contagious human pathogen and frequently causes worldwide outbreaks despite available vaccines. Similar to other mononegaviruses such as Ebola and rabies, MuV uses a single-stranded negative-sense RNA as its genome, which is enwrapped by viral nucleoproteins into the helical nucleocapsid. The nucleocapsid acts as a scaffold for genome condensation and as a template for RNA replication and transcription. Conformational changes in the MuV nucleocapsid are required to switch between different activities, but the underlying mechanism remains elusive due to the absence of high-resolution structures. Here, we report two MuV nucleoprotein-RNA rings with 13 and 14 protomers, one stacked-ring filament and two nucleocapsids with distinct helical pitches, in dense and hyperdense states, at near-atomic resolutions using cryo-electron microscopy. Structural analysis of these in vitro assemblies indicates that the C-terminal tail of MuV nucleoprotein likely regulates the assembly of helical nucleocapsids, and the C-terminal arm may be relevant for the transition between the dense and hyperdense states of helical nucleocapsids. Our results provide the molecular mechanism for structural plasticity among different MuV nucleocapsids and create a possible link between structural plasticity and genome condensation.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_database_related / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Nucleoprotein
B: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)63,2622
Polymers63,2622
Non-polymers00
Water0
1
A: Nucleoprotein
B: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
x 13


Theoretical massNumber of molelcules
Total (without water)822,40726
Polymers822,40726
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation12
Buried area1550 Å2
ΔGint-17 kcal/mol
Surface area18890 Å2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C13 (13 fold cyclic))

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Components

#1: Protein Nucleoprotein / / Nucleocapsid protein / NP / Protein N


Mass: 61470.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps virus (strain Jeryl-Lynn) / Strain: Jeryl-Lynn / Gene: N, NP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q77IS8
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps orthorubulavirus / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: Mumps virus nocleocapcid / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Mumps rubulavirus
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET28b
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris(hydroxymethyl)aminomethaneTris1
250 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 0.5 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: 277 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 FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Num. of particles: 390418 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å

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