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Yorodumi- PDB-6i54: Influenza A nucleoprotein docked into 3D helical structure of the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i54 | |||||||||
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Title | Influenza A nucleoprotein docked into 3D helical structure of the wild type ribonucleoprotein complex obtained using cryoEM. Conformation 2. | |||||||||
Components |
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Keywords | VIRAL PROTEIN / Influenza A virus Ribonucleoprotein RNA binding protein | |||||||||
Function / homology | Function and homology information negative stranded viral RNA replication / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / 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: 10 Å | |||||||||
Authors | Coloma, R. / Arranz, R. / de la Rosa-Trevin, J.M. / Sorzano, C.O.S. / Carlero, D. / Ortin, J. / Martin-Benito, J. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Structural insights into influenza A virus ribonucleoproteins reveal a processive helical track as transcription mechanism. Authors: Rocío Coloma / Rocío Arranz / José M de la Rosa-Trevín / Carlos O S Sorzano / Sandie Munier / Diego Carlero / Nadia Naffakh / Juan Ortín / Jaime Martín-Benito / Abstract: The influenza virus genome consists of eight viral ribonucleoproteins (vRNPs), each consisting of a copy of the polymerase, one of the genomic RNA segments and multiple copies of the nucleoprotein ...The influenza virus genome consists of eight viral ribonucleoproteins (vRNPs), each consisting of a copy of the polymerase, one of the genomic RNA segments and multiple copies of the nucleoprotein arranged in a double helical conformation. vRNPs are macromolecular machines responsible for messenger RNA synthesis and genome replication, that is, the formation of progeny vRNPs. Here, we describe the structural basis of the transcription process. The mechanism, which we call the 'processive helical track', is based on the extreme flexibility of the helical part of the vRNP that permits a sliding movement between both antiparallel nucleoprotein-RNA strands, thereby allowing the polymerase to move over the genome while bound to both RNA ends. Accordingly, we demonstrate that blocking this movement leads to inhibition of vRNP transcriptional activity. This mechanism also reveals a critical role of the nucleoprotein in maintaining the double helical structure throughout the copying process to make the RNA template accessible to the polymerase. | |||||||||
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 | 6i54.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i54.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i54_validation.pdf.gz | 743 KB | Display | wwPDB validaton report |
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Full document | 6i54_full_validation.pdf.gz | 785.5 KB | Display | |
Data in XML | 6i54_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 6i54_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/6i54 ftp://data.pdbj.org/pub/pdb/validation_reports/i5/6i54 | HTTPS FTP |
-Related structure data
Related structure data | 4412MC 0175C 4423C 4426C 4430C 6h9gC 6i7bC 6i7mC 6i85C C: citing same article (ref.) M: map data used to model this data |
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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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-Components
#1: Protein | Mass: 43079.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Influenza A virus (A/Wilson-Smith/1933(H1N1)) References: UniProt: Q1K9H2, UniProt: P15682*PLUS #2: Protein/peptide | Mass: 2107.346 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Influenza A virus (A/Wilson-Smith/1933(H1N1)) References: UniProt: P15682*PLUS |
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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: Influenza A virus / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Influenza A virus (A/Wilson-Smith/1933(H1N1)) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.4 / Details: TN buffer (50 mM Tris-HCl, 150 mM KCl) |
Buffer component | Conc.: 50 mM / Name: TN buffer / Formula: Tris-HCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: LEICA EM CPC / Cryogen name: ETHANE |
-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: 3000 nm / Nominal defocus min: 1500 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 2 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 420 |
Image scans | Movie frames/image: 69 / Used frames/image: 3-68 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -68.33 ° / Axial rise/subunit: 34.47 Å / Axial symmetry: D1 | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 137461 / Details: Manual picking | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 10 Å / Resolution method: OTHER / Num. of particles: 4806 / Algorithm: BACK PROJECTION Details: Local resolution calculated using MonoRes software. Vilas et al. Structure. 2018 Feb 6;26(2):337-344.e4. doi: 10.1016/j.str Num. of class averages: 1 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 2IQH Accession code: 2IQH / Source name: PDB / Type: experimental model |