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- PDB-8tkk: Cryo-EM structure of RNA device 43 truncation mutant 3 (U100C), a... -

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Basic information

Entry
Database: PDB / ID: 8tkk
TitleCryo-EM structure of RNA device 43 truncation mutant 3 (U100C), apo state
ComponentsRNA device 43 truncation mutant 3 (U100C)
KeywordsRNA / RNA device
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsStagno, J.R. / Deme, J.C. / Lee, Y.-T. / Wang, Y.-X. / Lea, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of RNA device 43 truncation mutant (U100C), apo state
Authors: Stagno, J.R. / Deme, J.C. / Lee, Y.-T. / Wang, Y.-X. / Lea, S.M.
History
DepositionJul 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA device 43 truncation mutant 3 (U100C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,28312
Polymers34,5171
Non-polymers76611
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain RNA device 43 truncation mutant 3 (U100C)


Mass: 34516.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: Synthetic RNA device containing hammerhead ribozyme and tetracycline-binding aptamer
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.035086 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 6.8
Buffer component
IDConc.NameBuffer-ID
110 mMBis-Tris1
2100 mMpotassium chloride1
31 mMmagnesium chloride1
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: in vitro transcribed RNA
Specimen supportDetails: 30s at 30mA on each side / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 284 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: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 54.5 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_4924 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 404781 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0022598
ELECTRON MICROSCOPYf_angle_d0.3224048
ELECTRON MICROSCOPYf_dihedral_angle_d16.2871295
ELECTRON MICROSCOPYf_chiral_restr0.014539
ELECTRON MICROSCOPYf_plane_restr0.001108

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