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- PDB-7eju: Junin virus(JUNV) RNA polymerase L complexed with Z protein -

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Basic information

Entry
Database: PDB / ID: 7eju
TitleJunin virus(JUNV) RNA polymerase L complexed with Z protein
Components
  • RING finger protein Z
  • RNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / Junin virus / RNA polymerase / L protein / Z protein
Function / homology
Function and homology information


negative stranded viral RNA replication / cap snatching / viral budding via host ESCRT complex / viral budding from plasma membrane / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / host cell perinuclear region of cytoplasm ...negative stranded viral RNA replication / cap snatching / viral budding via host ESCRT complex / viral budding from plasma membrane / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / host cell perinuclear region of cytoplasm / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / host cell plasma membrane / RNA binding / zinc ion binding / metal ion binding / membrane
Similarity search - Function
RING finger protein Z, zinc finger / RING finger protein Z, arenaviridae / Protein Z, RING-type zinc finger superfamily / P-11 zinc finger / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / : / 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 / RING finger protein Z
Similarity search - Component
Biological speciesJunin mammarenavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen, Y.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for recognition and regulation of arenavirus polymerase L by Z protein.
Authors: Huiling Kang / Jingyuan Cong / Chenlong Wang / Wenxin Ji / Yuhui Xin / Ying Qian / Xuemei Li / Yutao Chen / Zihe Rao /
Abstract: Junin virus (JUNV) causes Argentine hemorrhagic fever, a debilitating human disease of high mortality rates and a great risk to public health worldwide. Studying the L protein that replicates and ...Junin virus (JUNV) causes Argentine hemorrhagic fever, a debilitating human disease of high mortality rates and a great risk to public health worldwide. Studying the L protein that replicates and transcribes the genome of JUNV, and its regulator Z protein should provide critical clues to identify therapeutic targets for disrupting the life cycle of JUNV. Here we report the 3.54 Å cryo-EM structure of the JUNV L protein complexed with regulator Z protein. JUNV L structure reveals a conserved architecture containing signature motifs found in other L proteins. Structural analysis shows that L protein is regulated by binding of Z protein at the RNA product exit site. Based on these findings, we propose a model for the role of Z protein as a switch to turn on/off the viral RNA synthesis via its interaction with L protein. Our work unveils the mechanism of JUNV transcription, replication and regulation, which provides a framework for the rational design of antivirals for combating viral infections.
History
DepositionApr 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.0Jul 7, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 7, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 7, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 7, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 7, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 7, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 7, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.3Jun 18, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / Item: _em_admin.last_update

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: RING finger protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,1975
Polymers264,0422
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The JUNV L-Z protein complex elutes at ~15 ml on Superose 6 Increase 10/300 GL (GE healthcare)
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 253499.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Junin mammarenavirus / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: A0A0M4LRT1, RNA-directed RNA polymerase, Hydrolases; Acting on ester bonds
#2: Protein RING finger protein Z / Protein Z / Zinc-binding protein


Mass: 10542.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: matrix zinc binding protein of JUNV, which inactivates JUNV RNA polymerase
Source: (gene. exp.) Junin mammarenavirus / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q6IVU5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Complex of L and Z proteins of Junin virus (JUNV) / Type: COMPLEX
Details: The RNA polymerase L protein complexed with a zinc-binding Z protein
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Junin mammarenavirus
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 7.8 / Details: Solutions were made fresh.
Buffer component
IDConc.NameFormulaBuffer-ID
1500 mMsodium chlorideNaCl1
220 mMHEPESC8H18N2O4S1
31 mMTris(2-carboxyethyl)phosphine(TCEP)C9H16ClO6P1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportDetails: Frozen sample preparation begins immediately after glow discharge
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Num. of particles: 362657 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00913966
ELECTRON MICROSCOPYf_angle_d1.28118824
ELECTRON MICROSCOPYf_dihedral_angle_d14.3958524
ELECTRON MICROSCOPYf_chiral_restr0.0672137
ELECTRON MICROSCOPYf_plane_restr0.0082376

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