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Yorodumi- PDB-9cgi: Cryo-EM structure of the Nipah Virus polymerase (L) protein in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9cgi | ||||||
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Title | Cryo-EM structure of the Nipah Virus polymerase (L) protein in complex with the tetrameric phosphoprotein (P) | ||||||
Components |
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Keywords | TRANSFERASE / VIRAL PROTEIN / Nipah virus / L protein / phosphoprotein / RNA-dependent RNA polymerase / PRNTase / GDP polyribonucleotidyl transferase / RNA capping / viral replication | ||||||
Function / homology | Function and homology information negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / molecular adaptor activity / symbiont-mediated suppression of host innate immune response ...negative stranded viral RNA transcription / NNS virus cap methyltransferase / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / molecular adaptor activity / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / GTPase activity / ATP binding Similarity search - Function | ||||||
Biological species | Henipavirus nipahense | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å | ||||||
Authors | Liu, B. / Yang, G. / Wang, D. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure of the Nipah virus polymerase phosphoprotein complex. Authors: Yang, G. / Wang, D. / Liu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9cgi.cif.gz | 421.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9cgi.ent.gz | 311.5 KB | Display | PDB format |
PDBx/mmJSON format | 9cgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9cgi_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 9cgi_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 9cgi_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 9cgi_validation.cif.gz | 93.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/9cgi ftp://data.pdbj.org/pub/pdb/validation_reports/cg/9cgi | HTTPS FTP |
-Related structure data
Related structure data | 45580MC 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: 257565.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Henipavirus nipahense / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q997F0, RNA-directed RNA polymerase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, GDP polyribonucleotidyltransferase, NNS virus cap methyltransferase |
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#2: Protein | Mass: 78390.320 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Henipavirus nipahense / Gene: P/V/C / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9IK91 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The Nipah virus L-P complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.65 MDa / Experimental value: YES |
Source (natural) | Organism: Henipavirus nipahense |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 Details: 50 mM Tris-HCl pH 8.0, 250 mM NaCl, 5% glycerol, 1 mM TCEP, and 4 mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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 magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 63 K |
Image recording | Average exposure time: 1.7 sec. / Electron dose: 54.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6114 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software | Name: PHENIX / Version: 1.21_5207: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3052781 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278295 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 73.5 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||
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