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- PDB-5g2x: Structure a of Group II Intron Complexed with its Reverse Transcr... -

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Basic information

Entry
Database: PDB / ID: 5g2x
TitleStructure a of Group II Intron Complexed with its Reverse Transcriptase
Components
  • 5'-R(*CP*AP*CP*AP*UP*CP*CP*AP*UP*AP*AP*CP)-3'
  • GROUP II INTRON
  • GROUP II INTRON-ENCODED PROTEIN LTRA
KeywordsTRANSFERASE / GROUP II INTRONS / RIBONUCLEOPROTEIN / INTRON-ENCODED PROTEIN / RETROTRANSPOSONS AND SPLICEOSOM
Function / homology
Function and homology information


intron homing / RNA-directed DNA polymerase / mRNA processing / RNA-directed DNA polymerase activity / endonuclease activity / Hydrolases; Acting on ester bonds
Similarity search - Function
Domain X / : / Type II intron maturase / AI2M/AI1M-like, HNH endonuclease / : / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Group II intron-encoded protein LtrA
Similarity search - Component
Biological speciesLACTOCOCCUS LACTIS (lactic acid bacteria)
LACTOCOCCUS LACTIS SUBSP. CREMORIS (lactic acid bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3331
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: GROUP II INTRON
B: 5'-R(*CP*AP*CP*AP*UP*CP*CP*AP*UP*AP*AP*CP)-3'
C: GROUP II INTRON-ENCODED PROTEIN LTRA


Theoretical massNumber of molelcules
Total (without water)301,6533
Polymers301,6533
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: 227627.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Plasmid: PLNRK / Production host: LACTOCOCCUS LACTIS (lactic acid bacteria) / Strain (production host): IL1403
#2: RNA chain 5'-R(*CP*AP*CP*AP*UP*CP*CP*AP*UP*AP*AP*CP)-3'


Mass: 3739.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. CREMORIS (lactic acid bacteria)
Gene: LTRA, MATR / Plasmid: PLNRK / Production host: LACTOCOCCUS LACTIS (lactic acid bacteria) / Strain (production host): IL1403
#3: Protein GROUP II INTRON-ENCODED PROTEIN LTRA


Mass: 70286.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. CREMORIS (lactic acid bacteria)
Gene: LTRA, MATR / Plasmid: PLNRK / Production host: LACTOCOCCUS LACTIS (lactic acid bacteria) / Strain (production host): IL1403
References: UniProt: P0A3U0, RNA-directed DNA polymerase, Hydrolases; Acting on ester bonds

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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 / Type: COMPLEX / Details: MICROGRAPHS SELECTED BY EXAMINING CTF AND DRIFT
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 ETHANE

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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 magnification: 22500 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K / Tilt angle min: 0 °
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Num. of particles: 450296
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3331. (DEPOSITION ID: 14253).
Symmetry type: POINT
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 15075 0 0 19072

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