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- PDB-7f1m: Marburg virus nucleoprotein-RNA complex -

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Basic information

Entry
Database: PDB / ID: 7f1m
TitleMarburg virus nucleoprotein-RNA complex
Components
  • Nucleoprotein
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
KeywordsVIRAL PROTEIN / nucleoprotein
Function / homology
Function and homology information


viral RNA genome packaging / helical viral capsid / viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / RNA binding
Similarity search - Function
Ebola nucleoprotein / Ebola nucleoprotein
Similarity search - Domain/homology
Biological speciesLake Victoria marburgvirus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFujita, F.Y. / Sugita, Y. / Takamatsu, Y. / Houri, K. / Muramoto, Y. / Nakano, M. / Tsunoda, Y. / Igarashi, M. / Becker, S. / Noda, T.
Funding support Japan, 6items
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Movie
  • Biological unit as representative helical assembly
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-31420
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  • Superimposition on EM map
  • EMDB-31420
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
R: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
B: Nucleoprotein
S: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)91,9154
Polymers91,9154
Non-polymers00
Water0
1
A: Nucleoprotein
R: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
B: Nucleoprotein
S: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
x 63


Theoretical massNumber of molelcules
Total (without water)5,790,628252
Polymers5,790,628252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation62
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-35 kcal/mol
Surface area44180 Å2
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 63 / Rise per n subunits: 4.233 Å / Rotation per n subunits: -11.805 °)

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Components

#1: Protein Nucleoprotein / / Nucleocapsid protein


Mass: 44165.332 Da / Num. of mol.: 2 / Mutation: H198Y, H330Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Victoria marburgvirus (strain Angola/2005)
Strain: Angola/2005 / Gene: NP / Cell (production host): Suspension Cell Culture / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / Tissue (production host): Kidney (Embryonic) / References: UniProt: Q1PD53
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Marburgvirus nucleoprotein RNA complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium cholorideNaClSodium chloride1
21 mMEDTAEthylenediaminetetraacetic acid1
310 mMTris-HClTris1
SpecimenConc.: 1.47 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
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 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 FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 59000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2469
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1RELION3.1.0particle selection
2EPUimage acquisition
4GctfCTF correction
7Coot0.8.9.2model fitting
9RELION3.1.0initial Euler assignment
10RELION3.1.0final Euler assignment
11RELION3.1.0classification
12RELION3.1.03D reconstruction
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 30668
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23545 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 5Z9W

5z9w


Pdb chain-ID: A / Pdb chain residue range: 19-405

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