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- PDB-7ozr: Subtomogram average of authentic mumps virus nucleocapsid from He... -

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Basic information

Entry
Database: PDB / ID: 7ozr
TitleSubtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitch
Components
  • Nucleocapsid
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRUS / Helical filament / Nucleocapsid / Protein-RNA complex / Scaffold
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 genotype A
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.5 Å
AuthorsMahamid, J. / Zhang, X.
Funding supportEuropean Union, 1items
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, C.E. / Ching, C. / Pflaesterer, T. / Fung, H.K.H. / Poser, I. / Mueller, C.W. / Hyman, A.A. / Savitski, M.M. / Mahamid, J.
History
DepositionJun 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Database references / Refinement description / Category: citation / citation_author / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,1092
Polymers63,1092
Non-polymers00
Water00
1
A: Nucleocapsid
N: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
x 14


Theoretical massNumber of molelcules
Total (without water)883,52328
Polymers883,52328
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation13

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Components

#1: Protein Nucleocapsid / Nucleocapsid protein


Mass: 61316.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mumps virus genotype A / References: UniProt: A0A2Z4K4B8
#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 natural source / Source: (natural) Mumps virus genotype A

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Authentic Mumps virus nucleocapsid-RNA complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mumps virus genotype A
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: homo sap
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 2.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 8 / Used frames/image: 1-8

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Processing

SoftwareName: PHENIX / Version: 1.18_3845: / Classification: refinement
EM software
IDNameCategory
1Dynamovolume selection
2Warpvolume selection
3SerialEMimage acquisition
5WarpCTF correction
8UCSF Chimeramodel fitting
10PHENIXmodel refinement
11Cootmodel refinement
13RELIONfinal Euler assignment
14RELIONclassification
15RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -27.17 ° / Axial rise/subunit: 4.21 Å / Axial symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 939 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: HELICAL
EM volume selectionMethod: filament tracing / Num. of tomograms: 20 / Num. of volumes extracted: 939
Atomic model buildingB value: 56.3 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 4XJN

4xjn


Pdb chain-ID: A / Accession code: 4XJN / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 83.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053390
ELECTRON MICROSCOPYf_angle_d0.714617
ELECTRON MICROSCOPYf_dihedral_angle_d38.1951301
ELECTRON MICROSCOPYf_chiral_restr0.039520
ELECTRON MICROSCOPYf_plane_restr0.004587

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