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- EMDB-49355: Cryo-EM structure of Ro60/La/truncated misfolded human pre-5S rRN... -

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Basic information

Entry
Database: EMDB / ID: EMD-49355
TitleCryo-EM structure of Ro60/La/truncated misfolded human pre-5S rRNA complex with Fab, composite map
Map datacomposite map
Sample
  • Complex: Ro60/La/truncated misfolded human pre-5S rRNA/Fab
    • Protein or peptide: RNA-binding protein RO60
    • Protein or peptide: Lupus La protein
    • RNA: Truncated misfolded pre-5S rRNA
KeywordsRo60 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNam H / Deme JC / Lea SM / Wolin SL
Funding support United States, 2 items
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 JC / Sim S / Boccitto M / Lea SM / Wolin SL
History
DepositionFeb 21, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49355.png

Downloads & links

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Map

FileDownload / File: emd_49355.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å		0.73 Å/pix.
x 392 pix.
= 286.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.0018106845 - 2.1860867
Average (Standard dev.)0.0010817695 (±0.022292398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 286.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ro60/La/truncated misfolded human pre-5S rRNA/Fab

EntireName: Ro60/La/truncated misfolded human pre-5S rRNA/Fab
Components
  • Complex: Ro60/La/truncated misfolded human pre-5S rRNA/Fab
    • Protein or peptide: RNA-binding protein RO60
    • Protein or peptide: Lupus La protein
    • RNA: Truncated misfolded pre-5S rRNA

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Supramolecule #1: Ro60/La/truncated misfolded human pre-5S rRNA/Fab

SupramoleculeName: Ro60/La/truncated misfolded human pre-5S rRNA/Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RNA-binding protein RO60

MacromoleculeName: RNA-binding protein RO60 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.726523 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEESVNQMQP LNEKQIANSQ DGYVWQVTDM NRLHRFLCFG SEGGTYYIKE QKLGLENAEA LIRLIEDGRG CEVIQEIKSF SQEGRTTKQ EPMLFALAIC SQCSDISTKQ AAFKAVSEVC RIPTHLFTFI QFKKDLKESM KCGMWGRALR KAIADWYNEK G GMALALAV ...String:
MEESVNQMQP LNEKQIANSQ DGYVWQVTDM NRLHRFLCFG SEGGTYYIKE QKLGLENAEA LIRLIEDGRG CEVIQEIKSF SQEGRTTKQ EPMLFALAIC SQCSDISTKQ AAFKAVSEVC RIPTHLFTFI QFKKDLKESM KCGMWGRALR KAIADWYNEK G GMALALAV TKYKQRNGWS HKDLLRLSHL KPSSEGLAIV TKYITKGWKE VHELYKEKAL SVETEKLLKY LEAVEKVKRT KD ELEVIHL IEEHRLVREH LLTNHLKSKE VWKALLQEMP LTALLRNLGK MTANSVLEPG NSEVSLVCEK LCNEKLLKKA RIH PFHILI ALETYKTGHG LRGKLKWRPD EEILKALDAA FYKTFKTVEP TGKRFLLAVD VSASMNQRVL GSILNASTVA AAMC MVVTR TEKDSYVVAF SDEMVPCPVT TDMTLQQVLM AMSQIPAGGT DCSLPMIWAQ KTNTPADVFI VFTDNETFAG GVHPA IALR EYRKKMDIPA KLIVCGMTSN GFTIADPDDR GMLDMCGFDT GALDVIRNFT LDMI

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Macromolecule #2: Lupus La protein

MacromoleculeName: Lupus La protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.992273 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR LTTDFNVIVE ALSKSKAELM EISEDKTKI RRSPSKPLPE VTDEYKNDVK NRSVYIKGFP TDATLDDIKE WLEDKGQVLN IQMRRTLHKA FKGSIFVVFD S IESAKKFV ...String:
MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR LTTDFNVIVE ALSKSKAELM EISEDKTKI RRSPSKPLPE VTDEYKNDVK NRSVYIKGFP TDATLDDIKE WLEDKGQVLN IQMRRTLHKA FKGSIFVVFD S IESAKKFV ETPGQKYKET DLLILFKDDY FAKKNEERKQ NKVEAKLRAK QEQEAKQKLE EDAEMKSLEE KIGCLLKFSG DL DDQTCRE DLHILFSNHG EIKWIDFVRG AKEGIILFKE KAKEALGKAK DANNGNLQLR NKEVTWEVLE GEVEKEALKK IIE DQQESL NKWKSKGRRF KGKGKGNKAA QPGSGKGKVQ FQGKKTKFAS DDEHDEHDEN GATGPVKRAR EETDKEEPAS KQQK TENGA GDQLEHHHHH H

UniProtKB: Lupus La protein

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Macromolecule #3: Truncated misfolded pre-5S rRNA

MacromoleculeName: Truncated misfolded pre-5S rRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.207338 KDa
SequenceString:
GUCUACCCGC AUACCACCCU GUUCGCAGGG UCGGCGGUGG UCAGUACUUG CAAGGGUGCU GUAGGCUUUU UCUUUGGCUU UU

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333294
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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