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- PDB-5g2y: Structure a of Group II Intron Complexed with its Reverse Transcr... -

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Basic information

Entry
Database: PDB / ID: 5g2y
TitleStructure a of Group II Intron Complexed with its Reverse Transcriptase
ComponentsGROUP II INTRON
KeywordsTRANSFERASE / GROUP II INTRONS / RIBONUCLEOPROTEIN / INTRON-ENCODED PROTEIN / RETROTRANSPOSONS AND SPLICEOSOM
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsQu, G. / Kaushal, P.S. / Wang, J. / Shigematsu, H. / Piazza, C.L. / Agrawal, R.K. / Belfort, M. / Wang, H.W.
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Structure of a group II intron in complex with its reverse transcriptase.
Authors: Guosheng Qu / Prem Singh Kaushal / Jia Wang / Hideki Shigematsu / Carol Lyn Piazza / Rajendra Kumar Agrawal / Marlene Belfort / Hong-Wei Wang /
Abstract: Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as ...Bacterial group II introns are large catalytic RNAs related to nuclear spliceosomal introns and eukaryotic retrotransposons. They self-splice, yielding mature RNA, and integrate into DNA as retroelements. A fully active group II intron forms a ribonucleoprotein complex comprising the intron ribozyme and an intron-encoded protein that performs multiple activities including reverse transcription, in which intron RNA is copied into the DNA target. Here we report cryo-EM structures of an endogenously spliced Lactococcus lactis group IIA intron in its ribonucleoprotein complex form at 3.8-Å resolution and in its protein-depleted form at 4.5-Å resolution, revealing functional coordination of the intron RNA with the protein. Remarkably, the protein structure reveals a close relationship between the reverse transcriptase catalytic domain and telomerase, whereas the active splicing center resembles the spliceosomal Prp8 protein. These extraordinary similarities hint at intricate ancestral relationships and provide new insights into splicing and retromobility.
History
DepositionApr 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: GROUP II INTRON


Theoretical massNumber of molelcules
Total (without water)227,6111
Polymers227,6111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain GROUP II INTRON


Mass: 227611.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Production host: LACTOCOCCUS LACTIS (lactic acid bacteria) / References: RNA-directed DNA polymerase

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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: Group II Intron Complexed with its Reverse Transcriptase
Type: COMPLEX
Buffer solutionName: 50 MM TRIS-HCL, 10 MM KCL, 10 MM MGCL2, 5 MM DTT / pH: 7.5 / Details: 50 MM TRIS-HCL, 10 MM KCL, 10 MM MGCL2, 5 MM DTT
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID FREON

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Oct 1, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 2000

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Processing

CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Num. of particles: 102522
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3332. (DEPOSITION ID: 14254).
Symmetry type: POINT
RefinementHighest resolution: 4.5 Å
Refinement stepCycle: LAST / Highest resolution: 4.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 13494 0 0 13494

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