+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2867 | |||||||||
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Title | Structure of the helical Measles virus nucleocapsid | |||||||||
Map data | Reconstruction of trypsin digested Measles virus nucleocapsid | |||||||||
Sample |
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Keywords | Measles virus Nucleocapsid / Transcription and Replication template | |||||||||
Function / homology | Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / helical viral capsid / viral process / viral nucleocapsid / host cell cytoplasm / structural molecule activity / RNA binding / Nucleoprotein Function and homology information | |||||||||
Biological species | Measles virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Gutsche I / Desfosses A / Effantin G / Ling WL / Haupt M / Ruigrok RWH / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2867.map.gz | 30.3 MB | EMDB map data format | |
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Header (meta data) | emd-2867-v30.xml emd-2867.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | EMD-2867-image.png | 426 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2867 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2867 | HTTPS FTP |
-Validation report
Summary document | emd_2867_validation.pdf.gz | 331.4 KB | Display | EMDB validaton report |
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Full document | emd_2867_full_validation.pdf.gz | 330.6 KB | Display | |
Data in XML | emd_2867_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2867 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2867 | HTTPS FTP |
-Related structure data
Related structure data | 4uftMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2867.map.gz / Format: CCP4 / Size: 41.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of trypsin digested Measles virus nucleocapsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.186 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)
Entire | Name: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix) |
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Components |
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-Supramolecule #1000: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix)
Supramolecule | Name: Recombinant truncated Measles Virus Nucleocapsid (Ncore-RNA helix) type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 1 |
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-Macromolecule #1: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Details: Nucleoprotein was partially digested with trypsin / Oligomeric state: Helical / Recombinant expression: Yes |
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Source (natural) | Organism: Measles virus / Strain: Halle / synonym: Measles |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf21 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 7.5 / Details: in 20 mM TriHCl pH 7.5, 150 mM NaCl |
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Grid | Details: glow-discharged quantifoil grids 400 mesh 1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV Method: sample was applied to glow-discharged quantifoil grids 400 mesh 1.2/1.3, excess solution was blotted during 2 s with a Vitrobot Mark IV (FEI) and the grid frozen in liquid ethane |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Details | Special care was taken to perform a coma-free alignment of the microscope |
Date | Jul 1, 2013 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0035 µm / Nominal defocus min: 0.0008 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Final reconstruction obtained with SPRING |
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CTF correction | Details: Each Particle |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.015 Å Applied symmetry - Helical parameters - Δ&Phi: 29.173 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: OTHER / Software - Name: SPRING / Number images used: 228165 |