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- EMDB-62848: Structure of Ro60 dimer from Thermus phage phiLo -

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Basic information

Entry
Database: EMDB / ID: EMD-62848
TitleStructure of Ro60 dimer from Thermus phage phiLo
Map data
Sample
  • Complex: phiLoTrove in complex with Yrl2
    • Protein or peptide: TROVE domain-containing protein
    • RNA: RNA (62-MER)
KeywordsRo60 / trove / Rsr / Y-RNA / cryo-EM / protein-RNA complex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Function / homologyTROVE domain / TROVE domain superfamily / RNA-binding protein RO60 / TROVE domain profile. / von Willebrand factor A-like domain superfamily / ribonucleoprotein complex / RNA binding / metal ion binding / TROVE domain-containing protein
Function and homology information
Biological speciesThermus phage phiLo (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsHu Z / Huang Y
Funding support China, 2 items
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, 2024-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62848.png

Downloads & links

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Map

FileDownload / File: emd_62848.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 300 pix.
= 287.7 Å		0.96 Å/pix.
x 300 pix.
= 287.7 Å		0.96 Å/pix.
x 300 pix.
= 287.7 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.959 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.545662 - 0.7059537
Average (Standard dev.)-0.00020128941 (±0.0133019015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 287.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62848_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62848_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : phiLoTrove in complex with Yrl2

EntireName: phiLoTrove in complex with Yrl2
Components
  • Complex: phiLoTrove in complex with Yrl2
    • Protein or peptide: TROVE domain-containing protein
    • RNA: RNA (62-MER)

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Supramolecule #1: phiLoTrove in complex with Yrl2

SupramoleculeName: phiLoTrove in complex with Yrl2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus phage phiLo (virus)

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Macromolecule #1: TROVE domain-containing protein

MacromoleculeName: TROVE domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus phage phiLo (virus)
Molecular weightTheoretical: 57.038781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGL VPRGSHMETG TKTYEGAKAY KRSPHGELFT LVASSLFLGD NTYYEYGGER VERFINLATT LSKEDPEYVA SLANYARNE LGLRSNPAAL VAHLFYSNAL EERRDLILAT TKKVWQRGDD HLETLAYVKA VGWKLRSALK KAIAERLNDI P PSLLLKYK ...String:
HHHHHHSSGL VPRGSHMETG TKTYEGAKAY KRSPHGELFT LVASSLFLGD NTYYEYGGER VERFINLATT LSKEDPEYVA SLANYARNE LGLRSNPAAL VAHLFYSNAL EERRDLILAT TKKVWQRGDD HLETLAYVKA VGWKLRSALK KAIAERLNDI P PSLLLKYK RARRVVSQRL AIRLTHPRPR DEERSLLFQY IVKGSRASEE AKKLAEEVME ERPTWERIIS SKGSTPETWL EA LPHLNGL SLVRNLNNLF KHGLLENLEV KKTIEDKFSR SGSWKIFPFQ YYSALKMGEK EGWPYWIMAL LEEALESSAP ETR LEGETL FLVDVSGSMY YPVSRNSNLH MAEAASVLAT VLVKRLGGEL WTFADEAQDY TGHTHLSTYS LVRKIVREGR GGTY LERAI RKAILDRSWT GRRVVIITDE QTHDMPWEAL KDWLRSGENR VAHIINVAGY LPTAFPEDRI AKVGGWSDKI ITLIE SLEV GEEGIRNFLV SNYLPP

UniProtKB: TROVE domain-containing protein

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Macromolecule #2: RNA (62-MER)

MacromoleculeName: RNA (62-MER) / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Thermus phage phiLo (virus)
Molecular weightTheoretical: 20.096021 KDa
SequenceString:
UGCGCGAGGC GAAGCUAACU CUUUUCACUA AGGCUAGGAA GAGGAAAGAC GCUCCUCGGG GA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9kop

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47986
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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