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Yorodumi- PDB-4bbl: Cryo-electron microscopy reconstruction of the helical part of in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bbl | ||||||
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Title | Cryo-electron microscopy reconstruction of the helical part of influenza A virus ribonucleoprotein isolated from virions. | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / NUCLEOCAPSID | ||||||
Function / homology | Function and homology information negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | INFLUENZA A VIRUS | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 18 Å | ||||||
Model type details | P ATOMS ONLY, CHAIN Y, Z | ||||||
Authors | Arranz, R. / Coloma, R. / Chichon, F.J. / Conesa, J.J. / Carrascosa, J.L. / Valpuesta, J.M. / Ortin, J. / Martin-Benito, J. | ||||||
Citation | Journal: Science / Year: 2012 Title: The structure of native influenza virion ribonucleoproteins. Authors: Rocío Arranz / Rocío Coloma / Francisco Javier Chichón / José Javier Conesa / José L Carrascosa / José M Valpuesta / Juan Ortín / Jaime Martín-Benito / Abstract: The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with ...The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with the polymerase complex and nucleoprotein (NP), forming ribonucleoproteins (RNPs), which are responsible for virus transcription and replication. We describe the structure of native RNPs derived from virions. They show a double-helical conformation in which two NP strands of opposite polarity are associated with each other along the helix. Both strands are connected by a short loop at one end of the particle and interact with the polymerase complex at the other end. This structure will be relevant for unraveling the mechanisms of nuclear import of parental virus RNPs, their transcription and replication, and the encapsidation of progeny RNPs into virions. | ||||||
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 | 4bbl.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4bbl.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 4bbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bbl_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4bbl_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4bbl_validation.xml.gz | 314.3 KB | Display | |
Data in CIF | 4bbl_validation.cif.gz | 459.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/4bbl ftp://data.pdbj.org/pub/pdb/validation_reports/bb/4bbl | HTTPS FTP |
-Related structure data
Related structure data | 2205MC 2206C 2207C 2208C 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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-Components
#1: Protein | Mass: 56806.047 Da / Num. of mol.: 24 / Fragment: RESIDUES 8-498 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/WSN/33 (H1N1) Description: CRYOEM MAP FROM A/WSN/33 STRAND (H1N1). DOCKED PDB ID 2IQH. Cell line (production host): MDCK / Production host: CANIS LUPUS FAMILIARIS (dog) / References: UniProt: P15682, UniProt: Q1K9H2*PLUS #2: RNA chain | Mass: 94253.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS / Strain: A/WSN/33 (H1N1) Description: CRYOEM MAP FROM A/WSN/33 STRAND (H1N1). DOCKED PDB ID 2IQH. Cell line (production host): MDCK / Production host: CANIS LUPUS FAMILIARIS (dog) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: NATIVE INFLUENZA A VIRUS RIBONUCLEOPROTEIN (STRAIN A WSN 33, H1N1) Type: COMPLEX / Details: MICROGRAPHS SELECTED BY CTF QUALITY. |
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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: CARBON |
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- LEICA EM CPC, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jan 1, 2011 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 65000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.26 mm |
Image recording | Film or detector model: FEI EAGLE (4k x 4k) |
Image scans | Num. digital images: 559 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH PLATE | ||||||||||||||||||
3D reconstruction | Method: ITERATIVE HELICAL REAL SPACE RECONSTRUCTION PROTOCOL Resolution: 18 Å / Num. of particles: 876 / Nominal pixel size: 4.42 Å / Actual pixel size: 4.42 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2205.(DEPOSITION ID: 10953). Symmetry type: HELICAL | ||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: VOLUMETRIC / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||||
Atomic model building | PDB-ID: 2IQH Accession code: 2IQH / Source name: PDB / Type: experimental model | ||||||||||||||||||
Refinement | Highest resolution: 18 Å | ||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 18 Å
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