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Yorodumi- PDB-8pdr: Rigid body fit of assembled HMPV N-RNA spiral bound to the C-term... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pdr | ||||||
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Title | Rigid body fit of assembled HMPV N-RNA spiral bound to the C-terminal region of P | ||||||
Components |
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Keywords | VIRAL PROTEIN / Nucleoprotein / Virus / Nucleocapsid / RNA-binding / HMPV / Pneumoviridae / Mononegavirales | ||||||
Function / homology | Function and homology information helical viral capsid / virion component / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA-dependent RNA polymerase activity / RNA binding Similarity search - Function | ||||||
Biological species | Human metapneumovirus Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Whitehead, J.D. / Decool, H. / Leyrat, C. / Carrique, L. / Fix, J. / Eleouet, J.F. / Galloux, M. / Renner, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of the N-RNA/P interface indicates mode of L/P recruitment to the nucleocapsid of human metapneumovirus. Authors: Jack D Whitehead / Hortense Decool / Cédric Leyrat / Loic Carrique / Jenna Fix / Jean-François Eléouët / Marie Galloux / Max Renner / Abstract: Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and ...Human metapneumovirus (HMPV) is a major cause of respiratory illness in young children. The HMPV polymerase (L) binds an obligate cofactor, the phosphoprotein (P). During replication and transcription, the L/P complex traverses the viral RNA genome, which is encapsidated within nucleoproteins (N). An essential interaction between N and a C-terminal region of P tethers the L/P polymerase to the template. This N-P interaction is also involved in the formation of cytoplasmic viral factories in infected cells, called inclusion bodies. To define how the polymerase component P recognizes N-encapsidated RNA (N-RNA) we employed cryogenic electron microscopy (cryo-EM) and molecular dynamics simulations, coupled to activity assays and imaging of inclusion bodies in cells. We report a 2.9 Å resolution structure of a triple-complex between multimeric N, bound to both RNA and the C-terminal region of P. Furthermore, we also present cryo-EM structures of assembled N in different oligomeric states, highlighting the plasticity of N. Combined with our functional assays, these structural data delineate in molecular detail how P attaches to N-RNA whilst retaining substantial conformational dynamics. Moreover, the N-RNA-P triple complex structure provides a molecular blueprint for the design of therapeutics to potentially disrupt the attachment of L/P to its template. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pdr.cif.gz | 676.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pdr.ent.gz | 571.4 KB | Display | PDB format |
PDBx/mmJSON format | 8pdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/8pdr ftp://data.pdbj.org/pub/pdb/validation_reports/pd/8pdr | HTTPS FTP |
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-Related structure data
Related structure data | 17619MC 8pdlC 8pdmC 8pdnC 8pdoC 8pdpC 8pdqC 8pdsC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44534.570 Da / Num. of mol.: 11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human metapneumovirus (strain CAN97-83) Strain: CAN97-83 / Gene: N / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q6WBA1 #2: Protein/peptide | Mass: 1139.276 Da / Num. of mol.: 11 / Source method: obtained synthetically / Source: (synth.) Human metapneumovirus (strain CAN97-83) / References: UniProt: Q8B9Q8 #3: RNA chain | Mass: 2091.315 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: Rosetta2 |
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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
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 / Details: 12.5 mM Tris-HCl, pH 8.0, 125 mM NaCl | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 44.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Details: Please see publication for details | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201568 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Details: Rigid body only | ||||||||||||||||||||||||
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