+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18044 | |||||||||
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Title | Focused reconstruction of influenza A RNP-like particle | |||||||||
Map data | Focused reconstruction map post-processed. | |||||||||
Sample |
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Keywords | Influenza virus / Nucleocapsid-like / RNA binding protein. / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information 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 / synthetic construct (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||
Authors | Chenavier F / Estrozi LF / Zarkadas E / Ruigrok RWH / Schoehn G / Ballandras-Colas A / Crepin T | |||||||||
Funding support | France, 1 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Cryo-EM structure of influenza helical nucleocapsid reveals NP-NP and NP-RNA interactions as a model for the genome encapsidation. Authors: Florian Chenavier / Leandro F Estrozi / Jean-Marie Teulon / Eleftherios Zarkadas / Lily-Lorette Freslon / Jean-Luc Pellequer / Rob W H Ruigrok / Guy Schoehn / Allison Ballandras-Colas / Thibaut Crépin / Abstract: Influenza virus genome encapsidation is essential for the formation of a helical viral ribonucleoprotein (vRNP) complex composed of nucleoproteins (NP), the trimeric polymerase, and the viral genome. ...Influenza virus genome encapsidation is essential for the formation of a helical viral ribonucleoprotein (vRNP) complex composed of nucleoproteins (NP), the trimeric polymerase, and the viral genome. Although low-resolution vRNP structures are available, it remains unclear how the viral RNA is encapsidated and how NPs assemble into the helical filament specific of influenza vRNPs. In this study, we established a biological tool, the RNP-like particles assembled from recombinant influenza A virus NP and synthetic RNA, and we present the first subnanometric cryo-electron microscopy structure of the helical NP-RNA complex (8.7 to 5.3 Å). The helical RNP-like structure reveals a parallel double-stranded conformation, allowing the visualization of NP-NP and NP-RNA interactions. The RNA, located at the interface of neighboring NP protomers, interacts with conserved residues previously described as essential for the NP-RNA interaction. The NP undergoes conformational changes to enable RNA binding and helix formation. Together, our findings provide relevant insights for understanding the mechanism for influenza genome encapsidation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18044.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-18044-v30.xml emd-18044.xml | 23.1 KB 23.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18044_fsc.xml | 3.5 KB | Display | FSC data file |
Images | emd_18044.png | 50.7 KB | ||
Masks | emd_18044_msk_1.map | 4.5 MB | Mask map | |
Filedesc metadata | emd-18044.cif.gz | 7.1 KB | ||
Others | emd_18044_additional_1.map.gz emd_18044_half_map_1.map.gz emd_18044_half_map_2.map.gz | 2.3 MB 4.2 MB 4.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18044 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18044 | HTTPS FTP |
-Related structure data
Related structure data | 8pzqMC 8pzpC C: citing same article (ref.) M: atomic model generated by this map |
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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_18044.map.gz / Format: CCP4 / Size: 4.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Focused reconstruction map post-processed. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18044_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Focused reconstruction map non post-processed.
File | emd_18044_additional_1.map | ||||||||||||
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Annotation | Focused reconstruction map non post-processed. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1.
File | emd_18044_half_map_1.map | ||||||||||||
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Annotation | Half-map_1. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2.
File | emd_18044_half_map_2.map | ||||||||||||
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Annotation | Half-map_2. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Influenza A NP-RNA complex
Entire | Name: Influenza A NP-RNA complex |
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Components |
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-Supramolecule #1: Influenza A NP-RNA complex
Supramolecule | Name: Influenza A NP-RNA complex / 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: Influenza A virus |
-Supramolecule #3: RNA (5'P-(UC)6-FAM3')
Supramolecule | Name: RNA (5'P-(UC)6-FAM3') / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Nucleoprotein
Macromolecule | Name: Nucleoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Influenza A virus |
Molecular weight | Theoretical: 57.525965 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MATKGTKRSY EQMETDGERQ NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDP KKTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM D PRMCSLMQ ...String: MATKGTKRSY EQMETDGERQ NATEIRASVG KMIDGIGRFY IQMCTELKLS DYEGRLIQNS LTIERMVLSA FDERRNKYLE EHPSAGKDP KKTGGPIYRR VDGKWRRELI LYDKEEIRRI WRQANNGDDA TAGLTHMMIW HSNLNDATYQ RTRALVRTGM D PRMCSLMQ GSTLPRRSGA AGAAVKGVGT MVMELIRMIK RGINDRNFWR GENGRRTRIA YERMCNILKG KFQTAAQRTM VD QVRESRN PGNAEFEDLI FLARSALILR GSVAHKSCLP ACVYGSAVAS GYDFEREGYS LVGIDPFRLL QNSQVYSLIR PNE NPAHKS QLVWMACHSA AFEDLRVSSF IRGTKVVPRG KLSTRGVQIA SNENMETMES STLELRSRYW AIRTRSGGNT NQQR ASSGQ ISIQPTFSVQ RNLPFDRPTI MAAFTGNTEG RTSDMRTEII RLMESARPED VSFQGRGVFE LSDEKATSPI VPSFD MSNE GSYFFGDNAE EYDNLEHHHH HH UniProtKB: Nucleoprotein |
-Macromolecule #2: RNA (5'P-(UC)6-FAM3')
Macromolecule | Name: RNA (5'P-(UC)6-FAM3') / type: rna / ID: 2 / Number of copies: 2 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.623128 KDa |
Sequence | String: UCUCUCUCUC UC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.23 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: 20 mM HEPES 150 mM NaCl 5 mM beta-mercaptoethanol 2 mM methyl-PEG8-NHS | ||||||||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Details: 25 mA | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||
Details | 20 mM HEPES 150 mM NaCl 5 mM beta-mercaptoethanol Incubation overnight with 0.004 uM RNA (5'P-(UC)6-FAM3') Prior freezing, the sample was incubated 30 min on ice with 2 mM methyl-PEG8-NHS |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 26515 / Average exposure time: 1.9 sec. / Average electron dose: 40.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 21-490 / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Fitting of the NPcore by using ChimeraX |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-8pzq: |