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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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Open data


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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: Filippova EV / Krochmal D / Mukherjee S / Piccirilli JA / Kossiakoff AA
History
DepositionNov 14, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 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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