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- EMDB-50803: Cryo-EM structure of single-layered nucleoprotein-RNA helical ass... -

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Basic information

Entry
Database: EMDB / ID: EMD-50803
TitleCryo-EM structure of single-layered nucleoprotein-RNA helical assembly from Marburg virus, trimeric repeat unit
Map data
Sample
  • Complex: Helical assembly of nucleoprotein-RNA complex from Marburg virus
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
KeywordsRNA-binding protein / VIRAL PROTEIN
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein
Similarity search - Domain/homology
Biological speciesMarburg virus - Musoke, Kenya, 1980
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZinzula L / Beck F / Camasta M / Bohn S / Liu C / Morado D / Bracher A / Plitzko JM / Baumeister W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structure of single-layered nucleoprotein-RNA complex from Marburg virus.
Authors: Luca Zinzula / Florian Beck / Marianna Camasta / Stefan Bohn / Chuan Liu / Dustin Morado / Andreas Bracher / Juergen M Plitzko / Wolfgang Baumeister /
Abstract: Marburg virus (MARV) causes lethal hemorrhagic fever in humans, posing a threat to global health. We determined by cryogenic electron microscopy (cryo-EM) the MARV helical ribonucleoprotein (RNP) ...Marburg virus (MARV) causes lethal hemorrhagic fever in humans, posing a threat to global health. We determined by cryogenic electron microscopy (cryo-EM) the MARV helical ribonucleoprotein (RNP) complex structure in single-layered conformation, which differs from the previously reported structure of a double-layered helix. Our findings illuminate novel RNP interactions and expand knowledge on MARV genome packaging and nucleocapsid assembly, both processes representing attractive targets for the development of antiviral therapeutics against MARV disease.
History
DepositionJun 26, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50803.png

Downloads & links

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Map

FileDownload / File: emd_50803.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 476.16 Å		0.93 Å/pix.
x 512 pix.
= 476.16 Å		0.93 Å/pix.
x 512 pix.
= 476.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00243
Minimum - Maximum-0.009025586 - 0.013647945
Average (Standard dev.)0.000007109935 (±0.0006129704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 476.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50803_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50803_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50803_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Helical assembly of nucleoprotein-RNA complex from Marburg virus

EntireName: Helical assembly of nucleoprotein-RNA complex from Marburg virus
Components
  • Complex: Helical assembly of nucleoprotein-RNA complex from Marburg virus
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')

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Supramolecule #1: Helical assembly of nucleoprotein-RNA complex from Marburg virus

SupramoleculeName: Helical assembly of nucleoprotein-RNA complex from Marburg virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Marburg virus - Musoke, Kenya, 1980

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Marburg virus - Musoke, Kenya, 1980
Molecular weightTheoretical: 49.495105 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GMDLHSLLEL GTKPTAPHVR NKKVILFDTN HQVSICNQII DAINSGIDLG DLLEGGLLTL CVEHYYNSDK DKFNTSPIAK YLRDAGYEF DVIKNADATR FLDVIPNEPH YSPLILALKT LESTESQRGR IGLFLSFCSL FLPKLVVGDR ASIEKALRQV T VHQEQGIV ...String:
GMDLHSLLEL GTKPTAPHVR NKKVILFDTN HQVSICNQII DAINSGIDLG DLLEGGLLTL CVEHYYNSDK DKFNTSPIAK YLRDAGYEF DVIKNADATR FLDVIPNEPH YSPLILALKT LESTESQRGR IGLFLSFCSL FLPKLVVGDR ASIEKALRQV T VHQEQGIV TYPNHWLTTG HMKVIFGILR SSFILKFVLI HQGVNLVTGH DAYDSIISNS VGQTRFSGLL IVKTVLEFIL QK TDSGVTL HPLVRTSKVK NEVASFKQAL SNLARHGEYA PFARVLNLSG INNLEHGLYP QLSAIALGVA TAHGSTLAGV NVG EQYQQL REAAHDAEVK LQRRHEHQEI QAIAEDDEER KILEQFHLQK TEITHSQTLA VLSQKREKLA RLAAEIENNI VEDQ GFKQS QNRVSQSFLN DPTPVEVTVQ ARPMNRVEHH HHHHHH

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')

MacromoleculeName: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
type: rna / ID: 2 / Number of copies: 5
Source (natural)Organism: Marburg virus - Musoke, Kenya, 1980
Molecular weightTheoretical: 5.816651 KDa
SequenceString:
AGACACACAA AAACAAGA

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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

Concentration1.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 5518 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 2.86924 Å
Applied symmetry - Helical parameters - Δ&Phi: 14.732 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 12135
Segment selectionNumber selected: 67385 / Software - Name: crYOLO (ver. 1.7.6)
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9fvd:
Cryo-EM structure of single-layered nucleoprotein-RNA helical assembly from Marburg virus, trimeric repeat unit

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