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- PDB-6ueb: Structure of Rabies SAD-B19 L-P complex from cryo-EM -

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Basic information

Entry
Database: PDB / ID: 6ueb
TitleStructure of Rabies SAD-B19 L-P complex from cryo-EM
Components
  • Large structural protein
  • Phosphoprotein,Phosphoprotein
KeywordsVIRAL PROTEIN / Polymerase / Phosphoprotein / Complex
Function / homology
Function and homology information


NNS virus cap methyltransferase / symbiont-mediated suppression of host transcription / GDP polyribonucleotidyltransferase / microtubule-dependent intracellular transport of viral material towards nucleus / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component ...NNS virus cap methyltransferase / symbiont-mediated suppression of host transcription / GDP polyribonucleotidyltransferase / microtubule-dependent intracellular transport of viral material towards nucleus / negative stranded viral RNA replication / viral transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / virion component / host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTPase activity / virus-mediated perturbation of host defense response / host cell nucleus / ATP binding
Similarity search - Function
: / Virus-capping methyltransferase, C-terminal / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / : / Phosphoprotein / Phosphoprotein, C-terminal / Phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus ...: / Virus-capping methyltransferase, C-terminal / RNA-directed RNA polymerase, rhabdovirus / : / Virus-capping methyltransferase, connector domain / : / Phosphoprotein / Phosphoprotein, C-terminal / Phosphoprotein / RNA-directed RNA polymerase L methyltransferase domain, rhabdovirus / Virus-capping methyltransferase, MT domain / Mononegavirales RNA-directed RNA polymerase catalytic domain / Mononegavirus L protein 2-O-ribose methyltransferase / Mononegavirales mRNA-capping domain V / RNA-directed RNA polymerase L, C-terminal / Mononegavirales RNA dependent RNA polymerase / Mononegavirales mRNA-capping region V / RdRp of negative ssRNA viruses with non-segmented genomes catalytic domain profile. / Mononegavirus L protein 2'-O-ribose methyltransferase domain profile.
Similarity search - Domain/homology
Phosphoprotein / Large structural protein
Similarity search - Component
Biological speciesRabies virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHorwitz, J.A. / Harrison, S.C.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of a rabies virus polymerase complex from electron cryo-microscopy.
Authors: Joshua A Horwitz / Simon Jenni / Stephen C Harrison / Sean P J Whelan /
Abstract: Nonsegmented negative-stranded (NNS) RNA viruses, among them the virus that causes rabies (RABV), include many deadly human pathogens. The large polymerase (L) proteins of NNS RNA viruses carry all ...Nonsegmented negative-stranded (NNS) RNA viruses, among them the virus that causes rabies (RABV), include many deadly human pathogens. The large polymerase (L) proteins of NNS RNA viruses carry all of the enzymatic functions required for viral messenger RNA (mRNA) transcription and replication: RNA polymerization, mRNA capping, and cap methylation. We describe here a complete structure of RABV L bound with its phosphoprotein cofactor (P), determined by electron cryo-microscopy at 3.3 Å resolution. The complex closely resembles the vesicular stomatitis virus (VSV) L-P, the one other known full-length NNS-RNA L-protein structure, with key local differences (e.g., in L-P interactions). Like the VSV L-P structure, the RABV complex analyzed here represents a preinitiation conformation. Comparison with the likely elongation state, seen in two structures of pneumovirus L-P complexes, suggests differences between priming/initiation and elongation complexes. Analysis of internal cavities within RABV L suggests distinct template and product entry and exit pathways during transcription and replication.
History
DepositionSep 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Large structural protein
B: Phosphoprotein,Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,0284
Polymers247,8972
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4020 Å2
ΔGint-19 kcal/mol
Surface area86970 Å2

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Components

#1: Protein Large structural protein / Protein L / Replicase / Transcriptase


Mass: 243274.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus (strain SAD B19) / Strain: SAD B19 / Cell line (production host): SF-9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P16289, RNA-directed RNA polymerase, mRNA (guanine-N7)-methyltransferase, GDP polyribonucleotidyltransferase, EC: 2.1.1.296
#2: Protein/peptide Phosphoprotein,Phosphoprotein


Mass: 4623.038 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies virus (strain SAD B19) / Strain: SAD B19 / Cell line (production host): SF-9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16286
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rabies lyssavirus strain SAD-B19 L-P complex / Type: COMPLEX
Details: Purified L-P(1-91) complexes from baculovirus co-expression in insect cells
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rabies virus (strain SAD B19)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Strain: SF-9
Buffer solutionpH: 8.5
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 72 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44500
Details: cisTEM was used for the final reconstruction and FSC curve/resolution analysis.
Symmetry type: POINT

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