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- PDB-7alp: Severe fever with thrombocytopenia syndrome virus (Phenuiviridae)... -

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Basic information

Entry
Database: PDB / ID: 7alp
TitleSevere fever with thrombocytopenia syndrome virus (Phenuiviridae) L protein
ComponentsReplicase
KeywordsVIRAL PROTEIN / bunyavirus / L protein / phenuivirus / virus / polymerase / cap-snatching / enzyme
Function / homology
Function and homology information


host cell endoplasmic reticulum / virion component / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, PA-C-like domain / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesPhlebovirus WCH/97/HN/China/2011
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCusack, S. / Rosenthal, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Leibniz AssociationK27/2017 Germany
CitationJournal: Nat Microbiol / Year: 2021
Title: Errors in the deposited SFTSV L protein structure.
Authors: Stephen Cusack / Maria Rosenthal /
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 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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Structure viewerMolecule:
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Assembly

Deposited unit
U: Replicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,7593
Polymers235,7101
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area82900 Å2
MethodPISA

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Components

#1: Protein Replicase / Transcriptase


Mass: 235710.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phlebovirus WCH/97/HN/China/2011 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: I0DF35, RNA-directed RNA polymerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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: L protein of Severe fever with thrombocytopenia syndrome virus
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Severe fever with thrombocytopenia virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17_3644refinement
PHENIX1.17_3644refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147344 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 133.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003415697
ELECTRON MICROSCOPYf_angle_d0.620621173
ELECTRON MICROSCOPYf_chiral_restr0.04442357
ELECTRON MICROSCOPYf_plane_restr0.00332703
ELECTRON MICROSCOPYf_dihedral_angle_d21.00015883

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