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

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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
Specimen sourceLACTOCOCCUS LACTIS (lactic acid bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 16, 2016 / Release: May 4, 2016
RevisionDateData content typeGroupProviderType
1.0May 4, 2016Structure modelrepositoryInitial release
1.1May 11, 2016Structure modelDatabase references
1.2Jun 22, 2016Structure modelDatabase references

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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
Polyers227,6111
Non-polymers00
Water0
1


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: (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 / 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 / Details: 50 MM TRIS-HCL, 10 MM KCL, 10 MM MGCL2, 5 MM DTT / pH: 7.5
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
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Oct 1, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNumber digital images: 2000

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Processing

CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.5 Å / Number of particles: 102522
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3332. (DEPOSITION ID: 14254).
Symmetry type: POINT
Least-squares processHighest resolution: 4.5 Å
Refine hist #LASTHighest resolution: 4.5 Å
Number of atoms included #LASTProtein: 0 / Nucleic acid: 13494 / Ligand: 0 / Solvent: 0 / Total: 13494

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