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- PDB-9l5y: Structure of Ro60 dimer from Thermus phage phiLo -

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Basic information

Entry
Database: PDB / ID: 9l5y
TitleStructure of Ro60 dimer from Thermus phage phiLo
Components
  • RNA (62-MER)
  • TROVE domain-containing protein
KeywordsRNA BINDING PROTEIN/RNA / Ro60 / trove / Rsr / Y-RNA / cryo-EM / protein-RNA complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


ribonucleoprotein complex / RNA binding / metal ion binding
Similarity search - Function
TROVE domain / TROVE domain superfamily / RNA-binding protein RO60 / TROVE domain profile. / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / TROVE domain-containing protein
Similarity search - Component
Biological speciesThermus phage phiLo (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsHu, Z. / Huang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171186 China
National Natural Science Foundation of China (NSFC)91940302 China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural and molecular mechanisms of an Ro60 homolog from a Thermus bacteriophage.
Authors: Zetao Hu / Zhaohui Jin / Lulu Guo / Ling Zeng / Xuanjia Dong / Lin Jiang / Wenting Dai / Jinbiao Ma / Ying Huang /
Abstract: Ro60 is a conserved RNA-binding protein essential for RNA quality control and implicated in autoimmune responses. In this study, we present the structural and functional characterization of φRo60, ...Ro60 is a conserved RNA-binding protein essential for RNA quality control and implicated in autoimmune responses. In this study, we present the structural and functional characterization of φRo60, an Ro60 homolog from Thermus phage phiLo, with its crystal structure determined at 1.99 Å. Despite limited sequence identity with bacterial and amphibian homologs, φRo60 maintains the canonical doughnut-shaped architecture comprising HEAT repeats and a von Willebrand factor A domain. Surface electrostatic analysis reveals an extensive positively charged region across multiple α-helices, likely facilitating diverse RNA interactions. Moreover, φRo60 binds two Y RNA-like molecules (Yrl1 and Yrl2), identified from the phiLo genome, with distinct stoichiometries, leading to the formation of higher-order nucleocytoplasmic ribonucleoprotein (RNP) complexes. Cryo-electron microscopy of φRo60-Yrl2 RNP complexes revealed a minor population adopting a dimeric assembly, and key positively charged residues are important for φRo60-Yrl2 interactions. Additionally, φRo60 and Yrls interact with host Thermus thermophilus HB8 polynucleotide phosphorylase (PNPase), forming tripartite RYPER-like complexes and attenuating the ribonuclease activity of PNPase. These findings highlight φRo60 as a structurally adaptable Ro60 homolog capable of diverse RNA interactions and host factor recruitment, implying unique strategies for phages to counteract host defense systems in thermophilic environments.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROVE domain-containing protein
B: TROVE domain-containing protein
D: RNA (62-MER)
F: RNA (62-MER)


Theoretical massNumber of molelcules
Total (without water)154,2704
Polymers154,2704
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein TROVE domain-containing protein


Mass: 57038.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage phiLo (virus) / Gene: phiLo_26 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S7URH6
#2: RNA chain RNA (62-MER)


Mass: 20096.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus phage phiLo (virus) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: phiLoTrove in complex with Yrl2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermus phage phiLo (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47986 / Symmetry type: POINT
RefinementHighest resolution: 3.81 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038367
ELECTRON MICROSCOPYf_angle_d0.73411486
ELECTRON MICROSCOPYf_dihedral_angle_d15.3131559
ELECTRON MICROSCOPYf_chiral_restr0.041303
ELECTRON MICROSCOPYf_plane_restr0.0051333

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