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- PDB-9nfa: Cryo-EM structure of Ro60/La/minimal misfolded pre-5S rRNA comple... -

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Basic information

Entry
Database: PDB / ID: 9nfa
TitleCryo-EM structure of Ro60/La/minimal misfolded pre-5S rRNA complex with Fab, composite map
Components
  • Lupus La protein
  • Minimal misfolded pre-5S rRNA
  • RNA-binding protein RO60
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 / poly(U) RNA binding / tRNA processing / positive regulation of translation / cytoplasmic stress granule / tRNA binding / chromosome, telomeric region / ribonucleoprotein complex / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
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)
Xenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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(Cambridge,Mass.) / Year: 2026
Title: Mechanistic insights into RNA chaperoning by Ro60 and La autoantigens
Authors: Nam, H. / Deme, J.C. / Sim, S. / Boccitto, M. / Lea, S.M. / Wolin, S.L.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)129,1304
Polymers129,1063
Non-polymers241
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 Minimal misfolded pre-5S rRNA


Mass: 20386.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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/minimal misfolded pre-5S rRNA complex / Type: COMPLEX / Entity ID: #1-#3 / 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: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274169 / Symmetry type: POINT
RefinementHighest resolution: 2.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038241
ELECTRON MICROSCOPYf_angle_d0.56211325
ELECTRON MICROSCOPYf_dihedral_angle_d16.9551667
ELECTRON MICROSCOPYf_chiral_restr0.0381310
ELECTRON MICROSCOPYf_plane_restr0.0041253

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