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- EMDB-50804: Density for a protein trimer unit bound to RNA from a single-laye... -

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Basic information

Entry
Database: EMDB / ID: EMD-50804
TitleDensity for a protein trimer unit bound to RNA from a single-layered nucleoprotein-RNA helical assembly from Marburg virus
Map data
Sample
  • Complex: Helical assembly of nucleoprotein-RNA complex from Marburg virus
    • Protein or peptide: N protein from Marburg virus
    • RNA: RNA (5'-R(*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 / Marburg virus - Musoke
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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 11, 2024-
Current statusDec 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50804.png

Downloads & links

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Map

FileDownload / File: emd_50804.map.gz / Format: CCP4 / Size: 27 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 192 pix.
= 178.56 Å		0.93 Å/pix.
x 192 pix.
= 178.56 Å		0.93 Å/pix.
x 192 pix.
= 178.56 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: 0.00381
Minimum - Maximum-0.011353424 - 0.018403351
Average (Standard dev.)0.000011644853 (±0.0009453703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 178.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50804_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50804_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_50804_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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: N protein from Marburg virus
    • RNA: RNA (5'-R(*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: N protein from Marburg virus

MacromoleculeName: N protein from Marburg virus / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Marburg virus - Musoke
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GMDLHSLLEL GTKPTAPHVR NKKVILFDTN HQVSICNQII DAINSGIDLG DLLEGGLLTL CVEHYYNSDK DKFNTSPIAK YLRDAGYEFD VIKNADATRF LDVIPNEPHY SPLILALKTL ESTESQRGRI GLFLSFCSLF LPKLVVGDRA SIEKALRQVT VHQEQGIVTY ...String:
GMDLHSLLEL GTKPTAPHVR NKKVILFDTN HQVSICNQII DAINSGIDLG DLLEGGLLTL CVEHYYNSDK DKFNTSPIAK YLRDAGYEFD VIKNADATRF LDVIPNEPHY SPLILALKTL ESTESQRGRI GLFLSFCSLF LPKLVVGDRA SIEKALRQVT VHQEQGIVTY PNHWLTTGHM KVIFGILRSS FILKFVLIHQ GVNLVTGHDA YDSIISNSVG QTRFSGLLIV KTVLEFILQK TDSGVTLHPL VRTSKVKNEV ASFKQALSNL ARHGEYAPFA RVLNLSGINN LEHGLYPQLS AIALGVATAH GSTLAGVNVG EQYQQLREAA HDAEVKLQRR HEHQEIQAIA EDDEERKILE QFHLQKTEIT HSQTLAVLSQ KREKLARLAA EIENNIVEDQ GFKQSQNRVS QSFLNDPTPV EVTVQARPMN RVEHHHHHHH H

UniProtKB: Nucleoprotein

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

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

Concentration1.25 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClNaCl
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

Particle selectionNumber selected: 67385
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0)
Details: Final reconstruction was done on symmetry expanded and subtracted particles.
Number images used: 273909
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0)
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

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