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- EMDB-49353: Cryo-EM structure of Ro60/La/truncated misfolded human pre-5S rRN... -

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Basic information

Entry
Database: EMDB / ID: EMD-49353
TitleCryo-EM structure of Ro60/La/truncated misfolded human pre-5S rRNA complex with Fab, consensus map
Map datadeepEMhancer sharpened 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 human pre-5S rRNA
KeywordsRo60 autoantigen / RNA chaperone / RNA folding / La autoantigen / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
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_49353.png

Downloads & links

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Map

FileDownload / File: emd_49353.map.gz / Format: CCP4 / Size: 229.8 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.)
0.73 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: 0.05
Minimum - Maximum-0.0018352963 - 2.1860867
Average (Standard dev.)0.0008765006 (±0.020219468)
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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Mask #1

Fileemd_49353_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_49353_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: b-factor sharpened map

Fileemd_49353_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 2

Fileemd_49353_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_49353_half_map_2.map
Annotationhalf map 1
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/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 human 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 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEESVNQMQP LNEKQIANSQ DGYVWQVTDM NRLHRFLCFG SEGGTYYIKE QKLGLENAEA LIRLIEDGRG CEVIQEIKSF SQEGRTTKQE PMLFALAICS QCSDISTKQA AFKAVSEVCR IPTHLFTFIQ FKKDLKESMK CGMWGRALRK AIADWYNEKG GMALALAVTK ...String:
MEESVNQMQP LNEKQIANSQ DGYVWQVTDM NRLHRFLCFG SEGGTYYIKE QKLGLENAEA LIRLIEDGRG CEVIQEIKSF SQEGRTTKQE PMLFALAICS QCSDISTKQA AFKAVSEVCR IPTHLFTFIQ FKKDLKESMK CGMWGRALRK AIADWYNEKG GMALALAVTK YKQRNGWSHK DLLRLSHLKP SSEGLAIVTK YITKGWKEVH ELYKEKALSV ETEKLLKYLE AVEKVKRTKD ELEVIHLIEE HRLVREHLLT NHLKSKEVWK ALLQEMPLTA LLRNLGKMTA NSVLEPGNSE VSLVCEKLCN EKLLKKARIH PFHILIALET YKTGHGLRGK LKWRPDEEIL KALDAAFYKT FKTVEPTGKR FLLAVDVSAS MNQRVLGSIL NASTVAAAMC MVVTRTEKDS YVVAFSDEMV PCPVTTDMTL QQVLMAMSQI PAGGTDCSLP MIWAQKTNTP ADVFIVFTDN ETFAGGVHPA IALREYRKKM DIPAKLIVCG MTSNGFTIAD PDDRGMLDMC GFDTGALDVI RNFTLDMI

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Macromolecule #2: Lupus La protein

MacromoleculeName: Lupus La protein / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR LTTDFNVIVE ALSKSKAELM EISEDKTKIR RSPSKPLPEV TDEYKNDVKN RSVYIKGFPT DATLDDIKEW LEDKGQVLNI QMRRTLHKAF KGSIFVVFDS IESAKKFVET ...String:
MAENGDNEKM AALEAKICHQ IEYYFGDFNL PRDKFLKEQI KLDEGWVPLE IMIKFNRLNR LTTDFNVIVE ALSKSKAELM EISEDKTKIR RSPSKPLPEV TDEYKNDVKN RSVYIKGFPT DATLDDIKEW LEDKGQVLNI QMRRTLHKAF KGSIFVVFDS IESAKKFVET PGQKYKETDL LILFKDDYFA KKNEERKQNK VEAKLRAKQE QEAKQKLEED AEMKSLEEKI GCLLKFSGDL DDQTCREDLH ILFSNHGEIK WIDFVRGAKE GIILFKEKAK EALGKAKDAN NGNLQLRNKE VTWEVLEGEV EKEALKKIIE DQQESLNKWK SKGRRFKGKG KGNKAAQPGS GKGKVQFQGK KTKFASDDEH DEHDENGATG PVKRAREETD KEEPASKQQK TENGAGDQLE HHHHHH

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Macromolecule #3: Truncated misfolded human pre-5S rRNA

MacromoleculeName: Truncated misfolded human pre-5S rRNA / type: rna / ID: 3
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GUCUA Cccg C AUACC AC CCU G uucg CAGG GUCG G cggUG GU cAG UACUU gcaa GGGUG CUGUA GGC UU UUUCU U UGGC UUUU

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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
FSC plot (resolution estimation)

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