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- EMDB-13136: Subtomogram average of authentic mumps virus nucleocapsid from He... -

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Basic information

Entry
Database: EMDB / ID: EMD-13136
TitleSubtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of short helical pitch
Map dataMinor 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: Mumps virus nucleocapsid
    • RNA: RNA
KeywordsHelical filament / Nucleocapsid / Protein-RNA complex / Scaffold / VIRUS
Biological speciesMumps virus genotype A
Methodsubtomogram averaging / cryo EM / Resolution: 6.3 Å
AuthorsMahamid J / Zhang X / Pflaesterer T
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067European Union
CitationJournal: 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.
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_13136.png

Downloads & links

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Map

FileDownload / File: emd_13136.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMinor conformation of authentic mumps virus nucleocapsid from the lysate of HeLa cells after stress treatment by subtomogram averaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 256 pix.
= 433.613 Å		1.69 Å/pix.
x 256 pix.
= 433.613 Å		1.69 Å/pix.
x 256 pix.
= 433.613 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.6938 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-0.52652067 - 2.5432017
Average (Standard dev.)0.04158566 (±0.17538643)
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: Mumps virus nucleocapsid
    • RNA: RNA

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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: Mumps virus nucleocapsid

MacromoleculeName: Mumps virus nucleocapsid / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mumps virus genotype A / Strain: Enders
SequenceString: MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIRL ADRSPEAQIE RCEIDGFEPG TYRLIPNARA NLTANEIAAY ALLADDLPPT INNGTPYVHA DVEGQPCDEI EQFLDRCYSV ...String:
MSSVLKAFER FTIEQELQDR GEEGSIPPET LKSAVKVFVI NTPNPTTRYQ MLNFCLRIIC SQNARASHRV GALITLFSLP SAGMQNHIRL ADRSPEAQIE RCEIDGFEPG TYRLIPNARA NLTANEIAAY ALLADDLPPT INNGTPYVHA DVEGQPCDEI EQFLDRCYSV LIQAWVMVCK CMTAYDQPAG SADRRFAKYQ QQGRLEARYM LQPEAQRLIQ TAIRKSLVVR QYLTFELQLA RRQGLLSNRY YAMVGDIGKY IENSGLTAFF LTLKYALGTK WSPLSLAAFT GELTKLRSLM MLYRDIGEQA RYLALLEAPQ IMDFAPGGYP LIFSYAMGVG TVLDAQMRNY TYARPFLNGY YFQIGVETAR RQQGTVDNRV ADDLGLTPEQ RTEVTQLVDR LARGRGAGIP GGPVNPFVPP VQQQQPAAVY ADIPALEESD DDGDEDGGAG FQNGVQVPAV RQGGQTDFRA QPLQDPIQAQ LFMPLYPQVS NIPSNQNHQI NRIGGLENQD LLRYNENGDS QQDARGEHGN TFPNNPNQNA QLQVGDWDE

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2
Source (natural)Organism: Mumps virus genotype A
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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 3.51 Å
Applied symmetry - Helical parameters - Δ&Phi: -26.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number subtomograms used: 270
ExtractionNumber tomograms: 20 / Number images used: 270 / Method: filament tracing / Software: (Name: Dynamo, Warp)
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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