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- PDB-37so: tC19Z RNA polymerase ribozyme, apo state -

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Basic information

Entry
Database: PDB / ID: 37so
TitletC19Z RNA polymerase ribozyme, apo state
ComponentstC19Z RNA polymerase ribozyme
KeywordsRNA / synthetic / polymerase / ribozyme / apo
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHingey, J. / Spellmon, N. / Yu, Z. / Toor, N. / Rudolfs, B. / Mancino, A. / Haack, D.B. / Das, R.
Funding support United States, 4items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)2330652 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122579 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141706 United States
CitationJournal: To Be Published
Title: Predictive improvement of an RNA polymerase ribozyme from its substrate-free cryo-EM structure
Authors: Szokoli, D. / Hingey, J. / Zhiheng, Y. / Wu, V. / Toor, N. / Spellmon, N. / Rudolfs, B. / Mencino, A. / Haack, D.B. / Das, R.
History
DepositionAug 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tC19Z RNA polymerase ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,0636
Polymers194,9411
Non-polymers1225
Water45025
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 tC19Z RNA polymerase ribozyme


Mass: 194941.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tC19Z is inserted via L4 into a circularly permuted group II intron scaffold
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia phage T7 (virus)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: tC19Z RNA polymerase ribozyme / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia phage T7 (virus)
Buffer solutionpH: 6.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
3SerialEMimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152136 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0073941
ELECTRON MICROSCOPYf_angle_d0.7156134
ELECTRON MICROSCOPYf_dihedral_angle_d16.2811968
ELECTRON MICROSCOPYf_chiral_restr0.037825
ELECTRON MICROSCOPYf_plane_restr0.005165

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