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- EMDB-9105: Structure of a group II intron retroelement prior to DNA integration -

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Basic information

Entry
Database: EMDB / ID: EMD-9105
TitleStructure of a group II intron retroelement prior to DNA integration
Map data
SampleT.el4h group II intron retroelement:
(nucleic-acidNucleic acid) x 2 / Maturase reverse transcriptase / (ligand) x 2
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / nucleic acid binding / endonuclease activity
Reverse transcriptase domain / HNH endonuclease / HNH nuclease / Group II intron, maturase-specific / Reverse transcriptase, N-terminal domain / Group II intron reverse transcriptase/maturase / Reverse transcriptase (RNA-dependent DNA polymerase) / HNH endonuclease / Group II intron, maturase-specific domain / N-terminal domain of reverse transcriptase / Reverse transcriptase (RT) catalytic domain profile.
Maturase reverse transcriptase
Biological speciesThermosynechococcus elongatus (Cyanobacteria) / Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHaack D / Yan X / Zhang C / Hingey J / Lyumkis D / Baker TS / Toor N
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences1R01GM123275 United States
National Institutes of Health/Office of the DirectorDP5 OD021396 United States
National Institutes of Health/National Institute of General Medical Sciences1R01GM033050 United States
National Institutes of Health/National Institute of General Medical SciencesU54GM103368 United States
CitationJournal: Cell / Year: 2019
Title: Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.
Authors: Daniel B Haack / Xiaodong Yan / Cheng Zhang / Jason Hingey / Dmitry Lyumkis / Timothy S Baker / Navtej Toor /
Abstract: Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a ...Group II introns are a class of retroelements that invade DNA through a copy-and-paste mechanism known as retrotransposition. Their coordinated activities occur within a complex that includes a maturase protein, which promotes splicing through an unknown mechanism. The mechanism of splice site exchange within the RNA active site during catalysis also remains unclear. We determined two cryo-EM structures at 3.6-Å resolution of a group II intron reverse splicing into DNA. These structures reveal that the branch-site domain VI helix swings 90°, enabling substrate exchange during DNA integration. The maturase assists catalysis through a transient RNA-protein contact with domain VI that positions the branch-site adenosine for lariat formation during forward splicing. These findings provide the first direct evidence of the role the maturase plays during group II intron catalysis. The domain VI dynamics closely parallel spliceosomal branch-site helix movement and provide strong evidence for a retroelement origin of the spliceosome.
Validation ReportPDB-ID: 6me0

SummaryFull reportAbout validation report
History
DepositionSep 5, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseAug 14, 2019-
UpdateAug 14, 2019-
Current statusAug 14, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6me0
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9105.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 400 pix.
= 316. Å
0.79 Å/pix.
x 400 pix.
= 316. Å
0.79 Å/pix.
x 400 pix.
= 316. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.049953654 - 0.10808165
Average (Standard dev.)0.00021687546 (±0.0025322712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 316.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.790.790.79
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z316.000316.000316.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0500.1080.000

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Supplemental data

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Sample components

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Entire T.el4h group II intron retroelement

EntireName: T.el4h group II intron retroelement / Number of components: 6

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Component #1: protein, T.el4h group II intron retroelement

ProteinName: T.el4h group II intron retroelement / Recombinant expression: No
SourceSpecies: Thermosynechococcus elongatus (Cyanobacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: nucleic-acid, T.el4h RNA

nucleic acidName: T.el4h RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUGCGACGCG AAAGCUAGCC AGAUGAUUGU CCCACUAGCC CAACAAGCUA GAACGGGACC GGUUGUUCCC CCAACCGUAG CCUAGGGAGG CAUGCGUGAC UGGUAACGGU CAGGUGUGAA GCCCUCCCGA CAAUGUAGCC CGAACCGCAA GGUUGAAGCU GAAUCCGUGA GGAGGAAGCA ACUUCACCAG UGUCAGGUGA UAGGGAACUA GGCUUGAGGG UAUGGUGAGC ACAUGCGAAG UGAUGUCAGA AGCCUCGUCA CAGACCAACA GGCCAAAGAC ACUGAUAGGC CUGAGCCAAA ACGGCAAAUG GAUAGGCUAC AUCGCUCGCU CGUCGGUGUA CGGGGACGUC AAUCCAUCGG GGCACAGUCA CCACCUAACC CCUCGUGUCA UCUGGUUGGA ACGCGGUAAG CCCGUAUCCU CGCCUUGAAC ACUCAAGGCA GGCAAACCGU AAGGAAUGCU GAUGGGGGUG CGGGUAUGGG AUGCAGGAGA AAGCGAAUGC CGGUCUGUAA UGGACCGGAU AGGGGUUGAG GAGACAAUCC AACAUCACCC CGCCCGAAAG GGAGCAGACU UCCUGCUGGU CUCUCUUUGC GAGAUAGCCU GUAGAACCUC UUGAAUGGAG ACAAGGCAAA UGGCAGUGGA ACAAACCACU GGUGCGGUCA CCAACCAAAC GGAAACAAGC UGGCACAGCA UAGACUGGGC CAAAGCCAAC CGUGAGGUAA AGAGGCUGCA AGUGCGUAUC GCAAAGGCGU UCGCGCCGGU UCCUCUUGAA AGAGGGGCUU UGAGAGGCCU GAGCCGGAUG UGGGGAAACU CACAAGUCCG GUUCUUAGGG GGCGGGGAUG GCAGUAAUGC CUCCCUGCUA CCCGGC
MassTheoretical: 280.508812 kDa
SourceSpecies: Thermosynechococcus elongatus (Cyanobacteria)

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Component #3: nucleic-acid, Sense Target DNA

nucleic acidName: Sense Target DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DA)(DT)(DA)(DG)(DA)(DG)(DA)(DT)(DT) (DT)(DT)(DC)(DC)(DC)(DA)(DG)(DG)(DG)(DT) (DT)(DG)(DG)(DC)(DC)(DG)(DA)(DG)(DC)(DG) (DG)(DA)(DT)(DG)(DA)(DG)(DG)(DC)(DA)(DG) (DC)(DG)(DA)(DA)(DC)
MassTheoretical: 14.032991 kDa
SourceSpecies: Thermosynechococcus elongatus (Cyanobacteria)

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Component #4: protein, Maturase reverse transcriptase

ProteinName: Maturase reverse transcriptase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.065121 kDa
SourceSpecies: Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Strain: BP-1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 32 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #6: ligand, SODIUM ION

LigandName: SODIUM IONSodium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.29905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.1 mg/mL / pH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 58 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 73144
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 4R0D
Output model

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