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- EMDB-13133: Subtomogram average of authentic mumps virus nucleocapsid from He... -

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Basic information

Entry
Database: EMDB / ID: EMD-13133
TitleSubtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitch
Map dataMajor conformation of authentic mumps virus nucleocapsid from the lysate of HeLa cells after stress treatment by subtomogram averaging
Sample
  • Complex: Authentic Mumps virus nucleocapsid-RNA complex
    • Protein or peptide: NucleocapsidCapsid
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
KeywordsHelical filament / Nucleocapsid / Protein-RNA complex / Scaffold / VIRUS
Function / homologyParamyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / structural molecule activity / RNA binding / Nucleocapsid
Function and homology information
Biological speciesMumps virus genotype A
Methodsubtomogram averaging / cryo EM / Resolution: 4.5 Å
AuthorsMahamid J / Zhang X / Pflaesterer T
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067European Union
Citation
Journal: Cell / Year: 2023
Title: Molecular mechanisms of stress-induced reactivation in mumps virus condensates.
Authors: Xiaojie Zhang / Sindhuja Sridharan / Ievgeniia Zagoriy / Christina Eugster Oegema / Cyan Ching / Tim Pflaesterer / Herman K H Fung / Isabelle Becher / Ina Poser / Christoph W Müller / ...Authors: Xiaojie Zhang / Sindhuja Sridharan / Ievgeniia Zagoriy / Christina Eugster Oegema / Cyan Ching / Tim Pflaesterer / Herman K H Fung / Isabelle Becher / Ina Poser / Christoph W Müller / Anthony A Hyman / Mikhail M Savitski / Julia Mahamid /
Abstract: Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular ...Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular stress disrupts the metastable host-virus equilibrium in persistent infection and induces viral replication in a culture model of mumps virus. Using a combination of cell biology, whole-cell proteomics, and cryo-electron tomography, we show that persistent viral replication factories are dynamic condensates and identify the largely disordered viral phosphoprotein as a driver of their assembly. Upon stress, increased phosphorylation of the phosphoprotein at its interaction interface with the viral polymerase coincides with the formation of a stable replication complex. By obtaining atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events constitute a stress-mediated switch within viral condensates that provide an environment to support upregulation of viral replication.
#1: Journal: Biorxiv / Year: 2021
Title: Condensate-mediated reactivation of mumps virus infection under stress
Authors: Zhang X / Sridharan S / Zagoriy I / Oegema CE / Ching C / Pflaesterer T / Fung HKH / Poser I / Mueller CW / Hyman AA / Savitski MM / Mahamid J
History
DepositionJun 28, 2021-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13133.png

Downloads & links

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Map

FileDownload / File: emd_13133.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMajor conformation of authentic mumps virus nucleocapsid from the lysate of HeLa cells after stress treatment by subtomogram averaging
Voxel sizeX=Y=Z: 1.6938 Å
Density
Contour LevelBy AUTHOR: 0.72
Minimum - Maximum-1.1122935 - 2.7664142
Average (Standard dev.)0.030421112 (±0.15163046)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 433.6128 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Authentic Mumps virus nucleocapsid-RNA complex

EntireName: Authentic Mumps virus nucleocapsid-RNA complex
Components
  • Complex: Authentic Mumps virus nucleocapsid-RNA complex
    • Protein or peptide: NucleocapsidCapsid
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Authentic Mumps virus nucleocapsid-RNA complex

SupramoleculeName: Authentic Mumps virus nucleocapsid-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mumps virus genotype A

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Macromolecule #1: Nucleocapsid

MacromoleculeName: Nucleocapsid / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mumps virus genotype A
Molecular weightTheoretical: 61.316734 KDa
SequenceString: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR ANLTANEIAA YALLADDLPP TINNGTPYVH ADVEGQPCDE I EQFLDRCY ...String:
MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIR LADRSPEAQI ERCEIDGFEP GTYRLIPNAR ANLTANEIAA YALLADDLPP TINNGTPYVH ADVEGQPCDE I EQFLDRCY SVLIQAWVMV CKCMTAYDQP AGSADRRFAK YQQQGRLEAR YMLQPEAQRL IQTAIRKSLV VRQYLTFELQ LA RRQGLLS NRYYAMVGDI GKYIENSGLT AFFLTLKYAL GTKWSPLSLA AFTGELTKLR SLMMLYRDIG EQARYLALLE APQ IMDFAP GGYPLIFSYA MGVGTVLDAQ MRNYTYARPF LNGYYFQIGV ETARRQQGTV DNRVADDLGL TPEQRTEVTQ LVDR LARGR GAGIPGGPVN PFVPPVQQQQ PAAVYADIPA LEESDDDGDE DGGAGFQNGV QVPAVRQGGQ TDFRAQPLQD PIQAQ LFMP LYPQVSNIPS NQNHQINRIG GLENQDLLRY NENGDSQQDA RGEHGNTFPN NPNQNAQLQV GDWDE

UniProtKB: Nucleocapsid

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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Mumps virus genotype A
Molecular weightTheoretical: 1.792037 KDa
SequenceString:
UUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-8 / Average exposure time: 1.6 sec. / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 20 / Number images used: 939 / Method: filament tracing / Software: (Name: Dynamo, Warp)
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 4.21 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.17 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 939
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4xjn


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 56.3 / Target criteria: Correlation coefficient
Output model

PDB-7ozr:
Subtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitch

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