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Yorodumi- PDB-9fvd: Cryo-EM structure of single-layered nucleoprotein-RNA helical ass... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fvd | ||||||
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Title | Cryo-EM structure of single-layered nucleoprotein-RNA helical assembly from Marburg virus, trimeric repeat unit | ||||||
Components |
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Keywords | VIRAL 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 | ||||||
Biological species | Marburg virus - Musoke Kenya 1980 | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Zinzula, L. / Beck, F. / Camasta, M. / Bohn, S. / Liu, C. / Morado, D. / Bracher, A. / Plitzko, J.M. / Baumeister, W. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fvd.cif.gz | 227.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fvd.ent.gz | 183.2 KB | Display | PDB format |
PDBx/mmJSON format | 9fvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fvd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 9fvd_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 9fvd_validation.xml.gz | 59 KB | Display | |
Data in CIF | 9fvd_validation.cif.gz | 86.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/9fvd ftp://data.pdbj.org/pub/pdb/validation_reports/fv/9fvd | HTTPS FTP |
-Related structure data
Related structure data | 50803MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | Mass: 5816.651 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Marburg virus - Musoke, Kenya, 1980 Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Helical assembly of nucleoprotein-RNA complex from Marburg virus Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Marburg virus - Musoke, Kenya, 1980 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5518 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 14.732 ° / Axial rise/subunit: 2.86924 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 67385 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 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 building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model |