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- EMDB-73840: Cryo-EM structure of the open state of cIL RNA region at 4.3 A re... -

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Basic information

Entry
Database: EMDB / ID: EMD-73840
TitleCryo-EM structure of the open state of cIL RNA region at 4.3 A resolution
Map databox sharpened map in Phenix
Sample
  • Complex: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
    • RNA: RNA (155-MER)
KeywordsRNA / ribozyme / U1A / ribonucleoprotein (snRNP) complex
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsFilippova EV / Kossiakoff AA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: A universal Fab targeting a conserved U1A-RNA epitope for RNA structure determination by cryo-EM.
Authors: Ekaterina V Filippova / Daniel Krochmal / Somnath Mukherjee / Joseph A Piccirilli / Anthony A Kossiakoff /
Abstract: Recent advances in cryo-electron microscopy (cryo-EM) have made antigen-binding fragments (Fabs) essential tools in the field of structural biology. Fabs facilitate image alignment, thereby enhancing ...Recent advances in cryo-electron microscopy (cryo-EM) have made antigen-binding fragments (Fabs) essential tools in the field of structural biology. Fabs facilitate image alignment, thereby enhancing three-dimensional (3D) reconstruction, and increase the effective size of proteins, aiding in their structural elucidation. In this study, we sought to broaden the use of Fabs as fiducial markers to elucidate the structures of RNA molecules. Identifying an appropriate Fab for a specific RNA target can be particularly challenging due to RNA's inherent flexibility and tendency to assume multiple conformations, which complicate the process and prolong the structure determination timeline. To address this challenge, we designed a universal Fab that specifically recognizes a U1A-RNA epitope, thereby reducing the need for Fab selection tailored to each individual RNA target. We determined the cryo-EM structure of the class I ligase ribozyme complexed with a portable U1hpII loop bound to the U1A protein and the Fab. The resulting structure revealed that the Fab interacts with a conserved U1A-RNA binding region, which can be engineered into other RNA molecules. This strategy presents significant potential for streamlining the structural determination of various RNAs, which are essential for biological and biomedical research.
History
DepositionNov 14, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73840.png

Downloads & links

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Map

FileDownload / File: emd_73840.map.gz / Format: CCP4 / Size: 2.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbox sharpened map in Phenix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.89 Å/pix.
x 89 pix.
= 79.21 Å		0.89 Å/pix.
x 64 pix.
= 56.96 Å		0.89 Å/pix.
x 100 pix.
= 89. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 13.0
Minimum - Maximum-34.014296999999999 - 122.582809999999995
Average (Standard dev.)3.3989496 (±10.547601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin187112167
Dimensions6410089
Spacing8964100
CellA: 79.21 Å / B: 56.96 Å / C: 89.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73840_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73840_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73840_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex

EntireName: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
Components
  • Complex: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
    • RNA: RNA (155-MER)

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Supramolecule #1: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex

SupramoleculeName: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: RNA (155-MER)

MacromoleculeName: RNA (155-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.835676 KDa
SequenceString:
UCCAGUAGGA ACACUAUACU ACUGGAUAAU CAAAGACAAA UCUGCCCGAA GGGCUUGAGA ACAUAACCCA UUGCACUCCG GGUAUGCAG AGGUGGCAGC CUCCGGUGGG UUAAAACCCA ACGUUCUCAA CAAUAGUGAC CCAUUGCACU CCGGGU

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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

Concentration3 mg/mL
BufferpH: 7.4 / Details: 10 mM HEPES, 75 mM NaCl, 5 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 10696 / Average exposure time: 7.1 sec. / Average electron dose: 60.0 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: 0.9 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: OTHER / Details: Ab initio reconstruction by cryoSPARC.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
Details: The final map resolution was estimated based on the gold-standard Fourier Shell Correlation (FSC) using the 0.143 cut-off criterion as implemented in cryoSPARC
Number images used: 59244
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 6
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3hhn


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9z6i:
Cryo-EM structure of the open state of cIL RNA at 4.3 A resolution

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