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- EMDB-31420: Marburg virus nucleoprotein-RNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-31420
TitleMarburg virus nucleoprotein-RNA complex
Map data
Sample
  • Complex: Marburgvirus nucleoprotein RNA complex
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
Keywordsnucleoprotein / 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 speciesHomo sapiens (human) / Lake Victoria marburgvirus (strain Angola/2005) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFujita FY / Sugita Y
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03494 Japan
Japan Society for the Promotion of Science (JSPS)19K22529 Japan
Japan Society for the Promotion of Science (JSPS)19H04831 Japan
Japan Agency for Medical Research and Development (AMED)19fk0108113 Japan
Japan Agency for Medical Research and Development (AMED)20fk0108270h0001 Japan
Japan Science and TechnologyJPMJCR20HA Japan
CitationJournal: Nat Commun / Year: 2022
Title: Structural insight into Marburg virus nucleoprotein-RNA complex formation.
Authors: Yoko Fujita-Fujiharu / Yukihiko Sugita / Yuki Takamatsu / Kazuya Houri / Manabu Igarashi / Yukiko Muramoto / Masahiro Nakano / Yugo Tsunoda / Ichiro Taniguchi / Stephan Becker / Takeshi Noda /
Abstract: The nucleoprotein (NP) of Marburg virus (MARV), a close relative of Ebola virus (EBOV), encapsidates the single-stranded, negative-sense viral genomic RNA (vRNA) to form the helical NP-RNA complex. ...The nucleoprotein (NP) of Marburg virus (MARV), a close relative of Ebola virus (EBOV), encapsidates the single-stranded, negative-sense viral genomic RNA (vRNA) to form the helical NP-RNA complex. The NP-RNA complex constitutes the core structure for the assembly of the nucleocapsid that is responsible for viral RNA synthesis. Although appropriate interactions among NPs and RNA are required for the formation of nucleocapsid, the structural basis of the helical assembly remains largely elusive. Here, we show the structure of the MARV NP-RNA complex determined using cryo-electron microscopy at a resolution of 3.1 Å. The structures of the asymmetric unit, a complex of an NP and six RNA nucleotides, was very similar to that of EBOV, suggesting that both viruses share common mechanisms for the nucleocapsid formation. Structure-based mutational analysis of both MARV and EBOV NPs identified key residues for helical assembly and subsequent viral RNA synthesis. Importantly, most of the residues identified were conserved in both viruses. These findings provide a structural basis for understanding the nucleocapsid formation and contribute to the development of novel antivirals against MARV and EBOV.
History
DepositionJun 9, 2021-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7f1m
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7f1m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31420.png

Downloads & links

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Map

FileDownload / File: emd_31420.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.)
1.13 Å/pix.
x 512 pix.
= 578.56 Å		1.13 Å/pix.
x 512 pix.
= 578.56 Å		1.13 Å/pix.
x 512 pix.
= 578.56 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-2.03947 - 10.621826
Average (Standard dev.)0.000000000381426 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-255-255-255
Dimensions512512512
Spacing512512512
CellA=B=C: 578.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z578.560578.560578.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ330330330
MAP C/R/S123
start NC/NR/NS-255-255-255
NC/NR/NS512512512
D min/max/mean-2.03910.6220.000

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Supplemental data

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Mask #1

Fileemd_31420_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #2

Fileemd_31420_additional_1.map
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Half map: #2

Fileemd_31420_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_31420_half_map_2.map
Projections & Slices
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Sample components

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Entire : Marburgvirus nucleoprotein RNA complex

EntireName: Marburgvirus nucleoprotein RNA complex
Components
  • Complex: Marburgvirus nucleoprotein RNA complex
    • Protein or peptide: Nucleoprotein
    • RNA: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Marburgvirus nucleoprotein RNA complex

SupramoleculeName: Marburgvirus nucleoprotein RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Nucleoprotein

MacromoleculeName: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lake Victoria marburgvirus (strain Angola/2005) / Strain: Angola/2005
Molecular weightTheoretical: 44.165332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDLHSLLELG TKPTAPHVRN KKVILFDTNH QVSICNQIID AINSGIDLGD LLEGGLLTLC VEHYYNSDKD KFNTSPIAKY LRDAGYEFD VIKNADATRF LDVIPNEPHY SPLILALKTL ESTESQRGRI GLFLSFCSLF LPKLVVGDRA SIEKALRQVT V HQEQGIVT ...String:
MDLHSLLELG TKPTAPHVRN KKVILFDTNH QVSICNQIID AINSGIDLGD LLEGGLLTLC VEHYYNSDKD KFNTSPIAKY LRDAGYEFD VIKNADATRF LDVIPNEPHY SPLILALKTL ESTESQRGRI GLFLSFCSLF LPKLVVGDRA SIEKALRQVT V HQEQGIVT YPNHWLTTGH MKVIFGILRS SFILKFVLIY QGVNLVTGHD AYDSIISNSV GQTRFSGLLI VKTVLEFILQ KT DSGVTLH PLVRTSKVKN EVASFKQALS NLARHGEYAP FARVLNLSGI NNLEHGLYPQ LSAIALGVAT AHGSTLAGVN VGE QYQQLR EAAYDAEVKL QRRHEHQEIQ AIAEDDEERK ILEQFHLQKT EITHSQTLAV LSQKREKLAR LAAEIENNI

UniProtKB: Nucleoprotein

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Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.792037 KDa
SequenceString:
UUUUUU

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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

Concentration1.47 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium choloride
1.0 mMEDTA
10.0 mMTris-HCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Apply 1.25 micro littere of sample from each side of the grid and blot for 7 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2469 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 59000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
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

Particle selectionNumber selected: 30668
Startup modelType of model: OTHER / Details: cylinder created by relion_helix_toolbox
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 23545
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0) / Details: RELION 3D classification
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 6096 / Software - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5z9w


Chain - Chain ID: A / Chain - Residue range: 19-405 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7f1m:
Marburg virus nucleoprotein-RNA complex

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