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- EMDB-49329: Cryo-EM structure of Ro60/minimal misfolded pre-5S rRNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49329
TitleCryo-EM structure of Ro60/minimal misfolded pre-5S rRNA complex
Map datadeepEMhancer sharpened map
Sample
  • Complex: Ro60/minimal misfolded pre-5S rRNA complex
    • Protein or peptide: RNA-binding protein RO60
    • RNA: Minimal misfolded pre-5S rRNA
  • Ligand: MAGNESIUM ION
KeywordsRo60 autoantigen / RNA chaperone / RNA folding / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 20, 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_49329.png

Downloads & links

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Map

FileDownload / File: emd_49329.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 384 pix.
= 266.112 Å		0.69 Å/pix.
x 384 pix.
= 266.112 Å		0.69 Å/pix.
x 384 pix.
= 266.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.06667103 - 2.040176
Average (Standard dev.)0.0005938933 (±0.015987698)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 266.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49329_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_49329_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: B-factor sharpened map

Fileemd_49329_additional_2.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_49329_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_49329_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ro60/minimal misfolded pre-5S rRNA complex

EntireName: Ro60/minimal misfolded pre-5S rRNA complex
Components
  • Complex: Ro60/minimal misfolded pre-5S rRNA complex
    • Protein or peptide: RNA-binding protein RO60
    • RNA: Minimal misfolded pre-5S rRNA
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ro60/minimal misfolded pre-5S rRNA complex

SupramoleculeName: Ro60/minimal misfolded pre-5S rRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: Minimal misfolded pre-5S rRNA

MacromoleculeName: Minimal misfolded pre-5S rRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 20.38698 KDa
SequenceString:
GCCUACCCGC ACACUACCCU GUUCGCAGGG UCGGCGGUGG UUUUUCAUAG GCUUUUCAAA GUUU

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 49.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190106
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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