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- PDB-6u1x: Structure of the Vesicular Stomatitis Virus L Protein in Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u1x | ||||||
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Title | Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor (3.0 A resolution) | ||||||
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![]() | VIRAL PROTEIN / Vesicular stomatitis virus / RNA-dependent RNA polymerase / L protein / P protein / phosphoprotein / single particle analysis / transcription / replication / virus / viral / RdRp / PRNTase / nonsegmented negative-sense RNA viruses | ||||||
Function / homology | ![]() NNS virus cap methyltransferase / RNA folding chaperone / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / phosphorylation / viral genome replication / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...NNS virus cap methyltransferase / RNA folding chaperone / GDP polyribonucleotidyltransferase / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / phosphorylation / viral genome replication / virion component / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
![]() | Jenni, S. / Bloyet, L.M. / Dias-Avalos, R. / Liang, B. / Wheelman, S.P.J. / Grigorieff, N. / Harrison, S.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor. Authors: Simon Jenni / Louis-Marie Bloyet / Ruben Diaz-Avalos / Bo Liang / Sean P J Whelan / Nikolaus Grigorieff / Stephen C Harrison / ![]() Abstract: The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A ...The large (L) proteins of non-segmented, negative-strand RNA viruses are multifunctional enzymes that produce capped, methylated, and polyadenylated mRNA and replicate the viral genome. A phosphoprotein (P), required for efficient RNA-dependent RNA polymerization from the viral ribonucleoprotein (RNP) template, regulates the function and conformation of the L protein. We report the structure of vesicular stomatitis virus L in complex with its P cofactor determined by electron cryomicroscopy at 3.0 Å resolution, enabling us to visualize bound segments of P. The contacts of three P segments with multiple L domains show how P induces a closed, compact, initiation-competent conformation. Binding of P to L positions its N-terminal domain adjacent to a putative RNA exit channel for efficient encapsidation of newly synthesized genomes with the nucleoprotein and orients its C-terminal domain to interact with an RNP template. The model shows that a conserved tryptophan in the priming loop can support the initiating 5' nucleotide. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 709.8 KB | Display | ![]() |
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PDB format | ![]() | 573.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 20614MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 241313.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: San Juan / Production host: ![]() ![]() References: UniProt: P03523, RNA-directed RNA polymerase, mRNA (guanine-N7)-methyltransferase, GDP polyribonucleotidyltransferase, EC: 2.1.1.296 | ||
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#2: Protein | Mass: 29941.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: San Juan / Production host: ![]() ![]() | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: VSV L:P / Type: COMPLEX Details: L protein (full-length) in complex with P protein (35-106) Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.24 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 5 sec. / Electron dose: 100 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 3307 |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 50 / Used frames/image: 1-50 |
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Processing
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EM software |
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Image processing | Details: Movies were gain-corrected and aligned using cisTEM. | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF correction using cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 246825 / Details: Resolution limit for picking: 2 nm | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83979 / Algorithm: FOURIER SPACE Details: Refinement and classification were limited to a resolution of 0.4 nm to produce unbiased resolution estimate at final estimate resolution. Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 70.6 / Protocol: OTHER / Space: REAL / Target criteria: CC + restraints | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5A22 Pdb chain-ID: A / Accession code: 5A22 / Pdb chain residue range: 35-2109 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.67 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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