+Open data
-Basic information
Entry | Database: PDB / ID: 4uft | ||||||
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Title | Structure of the helical Measles virus nucleocapsid | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / MEASLES VIRUS NUCLEOCAPSID / TRANSCRIPTION AND REPLICATION TEMPLATE | ||||||
Function / homology | Function and homology information helical viral capsid / viral process / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding Similarity search - Function | ||||||
Biological species | MEASLES VIRUS STRAIN HALLE SPODOPTERA FRUGIPERDA (fall armyworm) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||
Authors | Gutsche, I. / Desfosses, A. / Effantin, G. / Ling, W.L. / Haupt, M. / Ruigrok, R.W.H. / Sachse, C. / Schoehn, G. | ||||||
Citation | Journal: Science / Year: 2015 Title: Structural virology. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid. Authors: Irina Gutsche / Ambroise Desfosses / Grégory Effantin / Wai Li Ling / Melina Haupt / Rob W H Ruigrok / Carsten Sachse / Guy Schoehn / Abstract: Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the ...Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the folded domain of the measles virus nucleoprotein encapsidating an RNA at a resolution of 4.3 angstroms. The resulting pseudoatomic model of the measles virus nucleocapsid offers important insights into the mechanism of the helical polymerization of nucleocapsids of negative-strand RNA viruses, in particular via the exchange subdomains of the nucleoprotein. The structure reveals the mode of the nucleoprotein-RNA interaction and explains why each nucleoprotein of measles virus binds six nucleotides, whereas the respiratory syncytial virus nucleoprotein binds seven. It provides a rational basis for further analysis of measles virus replication and transcription, and reveals potential targets for drug design. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4uft.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uft.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uft_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4uft_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4uft_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4uft_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/4uft ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4uft | HTTPS FTP |
-Related structure data
Related structure data | 2867MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 39 / Rise per n subunits: 4.015 Å / Rotation per n subunits: -29.173 °) |
-Components
#1: Protein | Mass: 43506.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NUCLEOPROTEIN WAS PARTIALLY DIGESTED WITH TRYPSIN / Source: (gene. exp.) MEASLES VIRUS STRAIN HALLE / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P10050 |
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#2: RNA chain | Mass: 1786.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPODOPTERA FRUGIPERDA (fall armyworm) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RECOMBINANT MEASLES NUCLEOPROTEIN-RNA HELICAL ASSEMBLY (NUCLEOCAPSID) Type: COMPLEX |
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Buffer solution | Name: IN 20 MM TRIHCL PH 7.5, 150 MM NACL / pH: 7.5 / Details: IN 20 MM TRIHCL PH 7.5, 150 MM NACL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Jul 1, 2013 Details: SPECIAL CARE WAS TAKEN TO PERFORM A COMA-FREE ALIGNMENT OF THE MICROSCOPE |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm |
Image recording | Film or detector model: KODAK SO-163 FILM |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE | ||||||||||||||||||
3D reconstruction | Method: WEIGHTED BACK-PROJECTION / Resolution: 4.3 Å / Num. of particles: 228165 / Nominal pixel size: 1.186 Å / Actual pixel size: 1.186 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2867. (DEPOSITION ID: 13046). Symmetry type: HELICAL | ||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||||
Atomic model building | PDB-ID: 2WJ8 Accession code: 2WJ8 / Source name: PDB / Type: experimental model | ||||||||||||||||||
Refinement | Highest resolution: 4.3 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.3 Å
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