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- EMDB-3333: Structure of a Group II Intron Complexed with its Reverse Transcr... -

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Basic information

Entry
Database: EMDB / ID: EMD-3333
TitleStructure of a Group II Intron Complexed with its Reverse Transcriptase
Map dataStructure a of Group II Intron Complexed with its Reverse Transcriptase, Without Mask
Sample
  • Sample: Structure a of Group II Intron Complexed with its Reverse Transcriptase
  • RNA: Group II Intron
  • Protein or peptide: Reverse Transcriptase
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 (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Group II intron-encoded protein LtrA
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsQu G / Kaushal PS / Wang J / Shigematsu H / Piazza CL / Agrawal RK / Belfort M / Wang HW
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
DepositionFeb 14, 2016-
Header (metadata) releaseFeb 24, 2016-
Map releaseMay 4, 2016-
UpdateJul 13, 2016-
Current statusJul 13, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3333.png

Downloads & links

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Map

FileDownload / File: emd_3333.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure a of Group II Intron Complexed with its Reverse Transcriptase, Without Mask
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å		1.31 Å/pix.
x 200 pix.
= 261.308 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.03828922 - 0.13209407
Average (Standard dev.)0.0007598 (±0.00519009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.308 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.308261.308261.308
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0380.1320.001

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Supplemental data

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Sample components

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Entire : Structure a of Group II Intron Complexed with its Reverse Transcr...

EntireName: Structure a of Group II Intron Complexed with its Reverse Transcriptase
Components
  • Sample: Structure a of Group II Intron Complexed with its Reverse Transcriptase
  • RNA: Group II Intron
  • Protein or peptide: Reverse Transcriptase

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Supramolecule #1000: Structure a of Group II Intron Complexed with its Reverse Transcr...

SupramoleculeName: Structure a of Group II Intron Complexed with its Reverse Transcriptase
type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 360 KDa / Theoretical: 360 KDa

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Macromolecule #1: Group II Intron

MacromoleculeName: Group II Intron / type: rna / ID: 1 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Lactococcus lactis (lactic acid bacteria)

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Macromolecule #2: Reverse Transcriptase

MacromoleculeName: Reverse Transcriptase / type: protein_or_peptide / ID: 2 / Recombinant expression: No
Source (natural)Organism: Lactococcus lactis (lactic acid bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

GridDetails: Quantifoil Cu-Rh R1.2/1.3 grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateOct 1, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 2266
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Software - Name: SPIDER, EMAN2, RELION / Number images used: 450296

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