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- EMDB-12918: Cryo-EM structure of the Cetacean morbillivirus nucleoprotein-RNA... -

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Basic information

Entry
Database: EMDB / ID: EMD-12918
TitleCryo-EM structure of the Cetacean morbillivirus nucleoprotein-RNA complex
Map dataMasked postprocessed map
Sample
  • Complex: Cetacean morbillivirus nucleoprotein-RNA complex
    • Complex: Cetacean morbillivirus nucleoprotein
      • Protein or peptide: Cetacean morbillivirus nucleoprotein
    • Complex: poly-A 6-mer
      • RNA: poly-A 6-mer
KeywordsCetacean morbillivirus / nucleocapsid / RNA virus replication / cryo-electron microscopy / helical reconstruction / single particle analysis / VIRAL PROTEIN
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 speciesMorbillivirus sp.
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsZinzula L / Beck F
CitationJournal: J Struct Biol / Year: 2021
Title: Cryo-EM structure of the cetacean morbillivirus nucleoprotein-RNA complex.
Authors: Luca Zinzula / Florian Beck / Sven Klumpe / Stefan Bohn / Günter Pfeifer / Daniel Bollschweiler / István Nagy / Jürgen M Plitzko / Wolfgang Baumeister /
Abstract: Cetacean morbillivirus (CeMV) is an emerging and highly infectious paramyxovirus that causes outbreaks in cetaceans and occasionally in pinnipeds, representing a major threat to biodiversity and ...Cetacean morbillivirus (CeMV) is an emerging and highly infectious paramyxovirus that causes outbreaks in cetaceans and occasionally in pinnipeds, representing a major threat to biodiversity and conservation of endangered marine mammal populations in both hemispheres. As for all non-segmented, negative-sense, single-stranded RNA (ssRNA) viruses, the morbilliviral genome is enwrapped by thousands of nucleoprotein (N) protomers. Each bound to six ribonucleotides, N protomers assemble to form a helical ribonucleoprotein (RNP) complex that serves as scaffold for nucleocapsid formation and as template for viral replication and transcription. While the molecular details on RNP complexes elucidated in human measles virus (MeV) served as paradigm model for these processes in all members of the Morbillivirus genus, no structural information has been obtained from other morbilliviruses, nor has any CeMV structure been solved so far. We report the structure of the CeMV RNP complex, reconstituted in vitro upon binding of recombinant CeMV N to poly-adenine ssRNA hexamers and solved to 4.0 Å resolution by cryo-electron microscopy. In spite of the amino acid sequence similarity and consequently similar folding of the N protomer, the CeMV RNP complex exhibits different helical parameters as compared to previously reported MeV orthologs. The CeMV structure reveals exclusive interactions leading to more extensive protomer-RNA and protomer-protomer interfaces. We identified twelve residues, among those varying between CeMV strains, as putatively important for the stabilization of the RNP complex, which highlights the need to study the potential of CeMV N mutations that modulate nucleocapsid assembly to also affect viral phenotype and host adaptation.
History
DepositionMay 11, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oi3
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7oi3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12918.png

Downloads & links

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Map

FileDownload / File: emd_12918.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked postprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.069292076 - 0.1053894
Average (Standard dev.)0.000047856687 (±0.003239362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.040279.040279.040
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.0690.1050.000

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Supplemental data

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Mask #1

Fileemd_12918_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: DeepEMhancer map

Fileemd_12918_additional_1.map
AnnotationDeepEMhancer map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Map before postprocessing

Fileemd_12918_additional_2.map
AnnotationMap before postprocessing
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_12918_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_12918_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cetacean morbillivirus nucleoprotein-RNA complex

EntireName: Cetacean morbillivirus nucleoprotein-RNA complex
Components
  • Complex: Cetacean morbillivirus nucleoprotein-RNA complex
    • Complex: Cetacean morbillivirus nucleoprotein
      • Protein or peptide: Cetacean morbillivirus nucleoprotein
    • Complex: poly-A 6-mer
      • RNA: poly-A 6-mer

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Supramolecule #1: Cetacean morbillivirus nucleoprotein-RNA complex

SupramoleculeName: Cetacean morbillivirus nucleoprotein-RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Cetacean morbillivirus nucleoprotein

SupramoleculeName: Cetacean morbillivirus nucleoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Morbillivirus sp.

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Supramolecule #3: poly-A 6-mer

SupramoleculeName: poly-A 6-mer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Morbillivirus sp.

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Macromolecule #1: Cetacean morbillivirus nucleoprotein

MacromoleculeName: Cetacean morbillivirus nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Morbillivirus sp.
Molecular weightTheoretical: 46.273625 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GMATLLRSLA LFKRNKDRTP LTAGSGGAIR GIKHVIVVPV PGDSSIVTRS RLLDRLVRLA GDPYISGPKL TGVMISILSL FVESPSQLI QRITDDPDVS IRLVEVIQSE KSLSGLTFAS RGANMEDEAD DYFSIQAGEE GDTRGTHWFE NKEIVEIEVQ D PEEFNILL ...String:
GMATLLRSLA LFKRNKDRTP LTAGSGGAIR GIKHVIVVPV PGDSSIVTRS RLLDRLVRLA GDPYISGPKL TGVMISILSL FVESPSQLI QRITDDPDVS IRLVEVIQSE KSLSGLTFAS RGANMEDEAD DYFSIQAGEE GDTRGTHWFE NKEIVEIEVQ D PEEFNILL ASILAQIWIL LAKAVTAPDT AADSETRRWI KYTQQRRVVG EFRLDKGWLD AVRNRIAEDL SLRRFMVALI LD IKRTPGN KPRIAEMICD IDTYIVEAGL ASFILTIKFG IETMYPALGL HEFSGELTTV ESLMNLYQQM GETAPYMVIL ENS IQNKFS AGSYPLLWSY AMGVGVELEN SMGGLNFGRS YFDPAYFRLG QEMVRRSAGK VSSSLAAELG ITAEDAKLVS EIAA QANDD RVEHHHHHHH H

UniProtKB: Nucleocapsid

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Macromolecule #2: poly-A 6-mer

MacromoleculeName: poly-A 6-mer / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Morbillivirus sp.
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloride
20.0 mMTris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 3153 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 22500
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 reconstructionApplied symmetry - Helical parameters - Δz: 5.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 28.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 31361
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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