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- PDB-9fvd: Cryo-EM structure of single-layered nucleoprotein-RNA helical ass... -

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Basic information

Entry
Database: PDB / ID: 9fvd
TitleCryo-EM structure of single-layered nucleoprotein-RNA helical assembly from Marburg virus, trimeric repeat unit
Components
  • Nucleoprotein
  • RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
KeywordsVIRAL PROTEIN / RNA-binding 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
RNA / RNA (> 10) / Nucleoprotein
Similarity search - Component
Biological speciesMarburg virus - Musoke
Kenya
1980
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZinzula, L. / Beck, F. / Camasta, M. / Bohn, S. / Liu, C. / Morado, D. / Bracher, A. / Plitzko, J.M. / Baumeister, W.
Funding support1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nucleoprotein
A: Nucleoprotein
C: Nucleoprotein
S: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
R: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
Q: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
U: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
T: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)177,5698
Polymers177,5698
Non-polymers00
Water00
1
B: Nucleoprotein
A: Nucleoprotein
C: Nucleoprotein
S: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
R: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
Q: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
U: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
T: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')

B: Nucleoprotein
A: Nucleoprotein
C: Nucleoprotein
S: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
R: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
Q: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
U: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
T: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')

B: Nucleoprotein
A: Nucleoprotein
C: Nucleoprotein
S: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
R: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
Q: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
U: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')
T: RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)532,70624
Polymers532,70624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 49495.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marburg virus - Musoke, Kenya, 1980 / Gene: NP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P27588
#2: RNA chain
RNA (5'-R(P*AP*GP*AP*CP*AP*CP*AP*CP*AP*AP*AP*AP*AP*CP*AP*AP*GP*A)-3')


Mass: 5816.651 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Marburg virus - Musoke, Kenya, 1980
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Helical assembly of nucleoprotein-RNA complex from Marburg virus
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Marburg virus - Musoke, Kenya, 1980
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMNaClNaCl1
SpecimenConc.: 1.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277.15 K

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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 FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5518

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Processing

EM software
IDNameVersionCategory
1crYOLO1.7.6particle selection
4CTFFIND4.1.14CTF correction
9RELION4initial Euler assignment
10RELION4final Euler assignment
12RELION43D reconstruction
13PHENIX1.19.2-4158_1309model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 14.732 ° / Axial rise/subunit: 2.86924 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 67385
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12135 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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