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Yorodumi- EMDB-17619: Rigid body fit of assembled HMPV N-RNA spiral bound to the C-term... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17619 | |||||||||
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Title | Rigid body fit of assembled HMPV N-RNA spiral bound to the C-terminal region of P | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nucleoprotein / Virus / Nucleocapsid / RNA-binding / HMPV / Pneumoviridae / Mononegavirales / VIRAL PROTEIN | |||||||||
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 (strain CAN97-83) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Whitehead JD / Decool H / Leyrat C / Carrique L / Fix J / Eleouet JF / Galloux M / Renner M | |||||||||
Funding support | United Kingdom, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17619.map.gz | 230 MB | EMDB map data format | |
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Header (meta data) | emd-17619-v30.xml emd-17619.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17619_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_17619.png | 96.2 KB | ||
Filedesc metadata | emd-17619.cif.gz | 6.2 KB | ||
Others | emd_17619_half_map_1.map.gz emd_17619_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17619 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17619 | HTTPS FTP |
-Validation report
Summary document | emd_17619_validation.pdf.gz | 978.5 KB | Display | EMDB validaton report |
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Full document | emd_17619_full_validation.pdf.gz | 978.1 KB | Display | |
Data in XML | emd_17619_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | emd_17619_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17619 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17619 | HTTPS FTP |
-Related structure data
Related structure data | 8pdrMC 8pdlC 8pdmC 8pdnC 8pdoC 8pdpC 8pdqC 8pdsC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17619.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_17619_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17619_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Spiral of assembled HMPV N-RNA bound to the C-terminal region of P
Entire | Name: Spiral of assembled HMPV N-RNA bound to the C-terminal region of P |
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Components |
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-Supramolecule #1: Spiral of assembled HMPV N-RNA bound to the C-terminal region of P
Supramolecule | Name: Spiral of assembled HMPV N-RNA bound to the C-terminal region of P type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Nucleoprotein
Supramolecule | Name: Nucleoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Human metapneumovirus (strain CAN97-83) / Strain: CAN97-83 |
-Supramolecule #3: RNA
Supramolecule | Name: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Supramolecule #4: Human metapneumovirus P C-terminal region
Supramolecule | Name: Human metapneumovirus P C-terminal region / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: Human metapneumovirus (strain CAN97-83) / Strain: CAN97-83 |
-Macromolecule #1: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Human metapneumovirus (strain CAN97-83) / Strain: CAN97-83 |
Molecular weight | Theoretical: 44.53457 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSLQGIHLSD LSYKHAILKE SQYTIKRDVG TTTAVTPSSL QQEITLLCGE ILYAKHADYK YAAEIGIQYI STALGSERVQ QILRNSGSE VQVVLTRTYS LGKIKNNKGE DLQMLDIHGV EKSWVEEIDK EARKTMATLL KESSGNIPQN QRPSAPDTPI I LLCVGALI ...String: MSLQGIHLSD LSYKHAILKE SQYTIKRDVG TTTAVTPSSL QQEITLLCGE ILYAKHADYK YAAEIGIQYI STALGSERVQ QILRNSGSE VQVVLTRTYS LGKIKNNKGE DLQMLDIHGV EKSWVEEIDK EARKTMATLL KESSGNIPQN QRPSAPDTPI I LLCVGALI FTKLASTIEV GLETTVRRAN RVLSDALKRY PRMDIPKIAR SFYDLFEQKV YHRSLFIEYG KALGSSSTGS KA ESLFVNI FMQAYGAGQT MLRWGVIARS SNNIMLGHVS VQAELKQVTE VYDLVREMGP ESGLLHLRQS PKAGLLSLAN CPN FASVVL GNASGLGIIG MYRGRVPNTE LFSAAESYAK SLKESNKINF SSLGLTDEEK EAAEHFLNVS DDSQNDYEKH HHHH H UniProtKB: Nucleoprotein |
-Macromolecule #2: Phosphoprotein
Macromolecule | Name: Phosphoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Human metapneumovirus (strain CAN97-83) |
Molecular weight | Theoretical: 1.139276 KDa |
Sequence | String: EDDIYQLIM UniProtKB: Phosphoprotein |
-Macromolecule #3: RNA
Macromolecule | Name: RNA / type: rna / ID: 3 / Number of copies: 11 |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: Rosetta2 |
Molecular weight | Theoretical: 2.091315 KDa |
Sequence | String: CCCCCCC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 / Details: 12.5 mM Tris-HCl, pH 8.0, 125 mM NaCl |
Grid | Model: Quantifoil R2/1 / Material: COPPER |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Rigid body only |
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Refinement | Protocol: RIGID BODY FIT |
Output model | PDB-8pdr: |