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- PDB-9nf8: Cryo-EM structure of Ro60/La/truncated misfolded human pre-5S rRN... -

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Basic information

Entry
Database: PDB / ID: 9nf8
TitleCryo-EM structure of Ro60/La/truncated misfolded human pre-5S rRNA complex with Fab, composite map
Components
  • Lupus La protein
  • RNA-binding protein RO60
  • Truncated misfolded pre-5S rRNA
KeywordsRNA BINDING PROTEIN/RNA / Ro60 autoantigen / RNA chaperone / RNA folding / La autoantigen / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / IRES-dependent viral translational initiation / RNA Polymerase III Transcription Termination / tRNA modification / tRNA export from nucleus / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal ...nuclear histone mRNA catabolic process / histone mRNA metabolic process / tRNA 3'-end processing / protein localization to cytoplasmic stress granule / IRES-dependent viral translational initiation / RNA Polymerase III Transcription Termination / tRNA modification / tRNA export from nucleus / RNA Polymerase III Abortive And Retractive Initiation / tRNA 5'-leader removal / sequence-specific mRNA binding / tRNA processing / poly(U) RNA binding / positive regulation of translation / cytoplasmic stress granule / tRNA binding / chromosome, telomeric region / ribonucleoprotein complex / mRNA binding / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RNA binding motif / Lupus La protein / La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif ...RNA binding motif / Lupus La protein / La protein, xRRM domain / xRRM domain profile. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Lupus La protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNam, H. / Deme, J.C. / Lea, S.M. / Wolin, S.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Wolin Group United States
CitationJournal: Cell / Year: 2026
Title: Mechanistic insights into RNA chaperoning by Ro60 and La autoantigens.
Authors: Hyeyeon Nam / Justin C Deme / Soyeong Sim / Marco Boccitto / Susan M Lea / Sandra L Wolin /
Abstract: Although ATP-independent chaperones assist RNA folding, the mechanisms by which they function remain elusive. Here, we demonstrate how two RNA chaperones collaborate to unfold misfolded noncoding ...Although ATP-independent chaperones assist RNA folding, the mechanisms by which they function remain elusive. Here, we demonstrate how two RNA chaperones collaborate to unfold misfolded noncoding RNAs (ncRNAs). The ring-shaped Ro60 protein binds the ends of misfolded ncRNAs in its cavity, whereas La stabilizes nascent ncRNAs and assists their folding. Using cryo-electron microscopy to resolve the structure of a misfolded RNA complexed with Ro60 and La, we show that La cradles the Ro60 ribonucleoprotein (RNP), with its N-terminal domain binding the RNA 3' end after it passes through the Ro60 cavity, while its C-terminal domain destabilizes structures in the misfolded RNA body. Using selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), we show that La and Ro60 function synergistically to unfold non-native structures. As the RNAs bound by Ro60 and La include both ncRNA precursors and ncRNAs with oligouridine tails, this RNA chaperone machine may function widely to recognize misfolded and otherwise aberrant ncRNAs and assist their unfolding.
History
DepositionFeb 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
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Revision 1.2Mar 4, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update
Revision 1.2Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-binding protein RO60
B: Lupus La protein
C: Truncated misfolded pre-5S rRNA


Theoretical massNumber of molelcules
Total (without water)134,9263
Polymers134,9263
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RNA-binding protein RO60


Mass: 60726.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RO60, SSA2, TROVE2 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Protein Lupus La protein / La autoantigen / La ribonucleoprotein / Sjoegren syndrome type B antigen / SS-B


Mass: 47992.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSB / Production host: Escherichia coli (E. coli) / References: UniProt: P05455
#3: RNA chain Truncated misfolded pre-5S rRNA


Mass: 26207.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
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: Ro60/La/truncated misfolded human pre-5S rRNA/Fab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60.3 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333294 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037945
ELECTRON MICROSCOPYf_angle_d0.48210889
ELECTRON MICROSCOPYf_dihedral_angle_d16.4181597
ELECTRON MICROSCOPYf_chiral_restr0.0371260
ELECTRON MICROSCOPYf_plane_restr0.0031212

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