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Yorodumi- PDB-2wfs: Fitting of influenza virus NP structure into the 9-fold symmetryz... -
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-Basic information
Entry | Database: PDB / ID: 2wfs | ||||||
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Title | Fitting of influenza virus NP structure into the 9-fold symmetryzed cryoEM reconstruction of an active RNP particle. | ||||||
Components | NUCLEOPROTEIN | ||||||
Keywords | VIRAL PROTEIN / VIRAL NUCLEOPROTEIN / HOST-VIRUS INTERACTION / RNA VIRUSES / NUCLEOPROTEIN / RIBONUCLEOPROTEIN / RNA / VIRION / NUCLEUS / INFLUENZA / RNA-BINDING | ||||||
Function / homology | Function and homology information cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus ...cRNA Synthesis / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / vRNA Synthesis / Transport of Ribonucleoproteins into the Host Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / vRNP Assembly / Viral Messenger RNA Synthesis / helical viral capsid / Viral mRNA Translation / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / host cell nucleus / structural molecule activity / RNA binding / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | INFLUENZA A VIRUS | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å | ||||||
Authors | Coloma, R. / Valpuesta, J.M. / Arranz, R. / Carrascosa, J.L. / Ortin, J. / Martin-Benito, J. | ||||||
Citation | Journal: PLoS Pathog / Year: 2009 Title: The structure of a biologically active influenza virus ribonucleoprotein complex. Authors: Rocío Coloma / José M Valpuesta / Rocío Arranz / José L Carrascosa / Juan Ortín / Jaime Martín-Benito / Abstract: The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein ...The influenza viruses contain a segmented, single-stranded RNA genome of negative polarity. Each RNA segment is encapsidated by the nucleoprotein and the polymerase complex into ribonucleoprotein particles (RNPs), which are responsible for virus transcription and replication. Despite their importance, information about the structure of these RNPs is scarce. We have determined the three-dimensional structure of a biologically active recombinant RNP by cryo-electron microscopy. The structure shows a nonameric nucleoprotein ring (at 12 Angstrom resolution) with two monomers connected to the polymerase complex (at 18 Angstrom resolution). Docking the atomic structures of the nucleoprotein and polymerase domains, as well as mutational analyses, has allowed us to define the interactions between the functional elements of the RNP and to propose the location of the viral RNA. Our results provide the first model for a functional negative-stranded RNA virus ribonucleoprotein complex. The structure reported here will serve as a framework to generate a quasi-atomic model of the molecular machine responsible for viral RNA synthesis and to test new models for virus RNA replication and transcription. | ||||||
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 | 2wfs.cif.gz | 462.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wfs.ent.gz | 282.6 KB | Display | PDB format |
PDBx/mmJSON format | 2wfs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wfs_validation.pdf.gz | 839.8 KB | Display | wwPDB validaton report |
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Full document | 2wfs_full_validation.pdf.gz | 852.3 KB | Display | |
Data in XML | 2wfs_validation.xml.gz | 76.4 KB | Display | |
Data in CIF | 2wfs_validation.cif.gz | 118.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfs ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfs | HTTPS FTP |
-Related structure data
Related structure data | 1603MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 56806.047 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/VICTORIA/3/75 (H3N2) / Gene: NP / Organ (production host): KIDNEY / Production host: CHLOROCEBUS AETHIOPS (grivet) / References: UniProt: P03466*PLUS |
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-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: INFLUENZA VIRUS RIBONUCLEOPROTEIN PARTICLE / Type: VIRUS Details: MICROGRAPHS SELECTED BY COMPUTED CTF DATA AQUISITION |
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Buffer solution | Name: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL, 150MM IMIDAZOLE pH: 8 Details: 50MM TRIS-HCL,100MM KCL, 5MM MGCL2,0.5% IGEPAL, 150MM IMIDAZOLE |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Details: CRYOGEN - ETHANE INSTRUMENT - LEICA PLUNGER |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 20 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.26 mm |
Specimen holder | Temperature: 99 K |
Image recording | Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 159 |
-Processing
EM software |
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CTF correction | Details: WHOLE PLATE | ||||||||||||
Symmetry | Point symmetry: C9 (9 fold cyclic) | ||||||||||||
3D reconstruction | Method: ANGULAR RECONSTITUTION,ITERATIVE ALGEBRAIC RECONSTRUCTION Resolution: 12 Å / Num. of particles: 9571 / Actual pixel size: 2.8 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1603. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: VOLUMETRIC / Details: METHOD--RIGID BODY | ||||||||||||
Atomic model building | PDB-ID: 2IQH Accession code: 2IQH / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 12 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 12 Å
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