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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: Zinzula, L. / Beck, F. / Camasta, M. / Bohn, S. / Liu, C. / Morado, D. / Bracher, A. / Plitzko, J.M. / Baumeister, W.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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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


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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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