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

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Open data


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Basic information

Entry
Database: PDB / ID: 9z6i
TitleCryo-EM structure of the open state of cIL RNA at 4.3 A resolution
ComponentsRNA (155-MER)
KeywordsRNA / ribozyme / U1A / ribonucleoprotein (snRNP) complex
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsFilippova, E.V. / Kossiakoff, A.A.
Funding support United States, 1items
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, E.V. / Krochmal, D. / Mukherjee, S. / Piccirilli, J.A. / Kossiakoff, A.A.
History
DepositionNov 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (155-MER)


Theoretical massNumber of molelcules
Total (without water)49,8361
Polymers49,8361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNA (155-MER)


Mass: 49835.676 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RNA was produced in vitro by transcribing a synthetic DNA construct using T7 RNA polymerase from a linearized pUC307HP plasmid
Source: (synth.) synthetic construct (others)
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 7.4 / Details: 10 mM HEPES, 75 mM NaCl, 5 mM MgCl2
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm
Image recordingAverage exposure time: 7.1 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10696

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.32 Å / Resolution method: OTHER / Num. of particles: 59244
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
Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 3hhn

3hhn


Accession code: 3hhn / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.32 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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