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- EMDB-26549: CryoEM Structure of an Group II Intron Retroelement (apo-complex) -

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Basic information

Entry
Database: EMDB / ID: EMD-26549
TitleCryoEM Structure of an Group II Intron Retroelement (apo-complex)
Map dataApoRNP Full Consensus Map
Sample
  • Complex: Complex of RNA and protein
    • RNA: E.r IIC Intron
    • Protein or peptide: Group II intron reverse transcriptase/maturase
  • Ligand: MAGNESIUM ION
  • Ligand: AMMONIUM ION
KeywordsRNA / intron / group II / maturase / splicing / retrotransposition / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


RNA-directed DNA polymerase / RNA-directed DNA polymerase activity
Similarity search - Function
Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / : / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Group II intron reverse transcriptase/maturase
Similarity search - Component
Biological species[Eubacterium] rectale (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChung K / Xu L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
Title: Structures of a mobile intron retroelement poised to attack its structured DNA target.
Authors: Kevin Chung / Ling Xu / Pengxin Chai / Junhui Peng / Swapnil C Devarkar / Anna Marie Pyle /
Abstract: Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam ...Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam the genome, integrating by reversal of forward splicing. Here we show that retrotransposition is achieved by a tertiary complex between a structurally elaborate ribozyme, its protein mobility factor, and a structured DNA substrate. We solved cryo-electron microscopy structures of an intact group IIC intron-maturase retroelement that was poised for integration into a DNA stem-loop motif. By visualizing the RNP before and after DNA targeting, we show that it is primed for attack and fits perfectly with its DNA target. This study reveals design principles of a prototypical retroelement and reinforces the hypothesis that group II introns are ancient elements of genetic diversification.
History
DepositionMar 29, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26549.png

Downloads & links

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Map

FileDownload / File: emd_26549.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApoRNP Full Consensus Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.14539893 - 0.42524138
Average (Standard dev.)0.0006854515 (±0.014867386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26549_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_26549_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ApoRNP Focused Refined (Left) Map

Fileemd_26549_additional_1.map
AnnotationApoRNP Focused Refined (Left) Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ApoRNP Focused Refined (Right) Map

Fileemd_26549_additional_2.map
AnnotationApoRNP Focused Refined (Right) Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Additional map: ApoRNP Composite Map

Fileemd_26549_additional_3.map
AnnotationApoRNP Composite Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ApoRNP Focused Refined (Left) Half Map A

Fileemd_26549_additional_4.map
AnnotationApoRNP Focused Refined (Left) Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ApoRNP Focused Refined (Left) Half Map B

Fileemd_26549_additional_5.map
AnnotationApoRNP Focused Refined (Left) Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ApoRNP Focused Refined (Right) Half Map A

Fileemd_26549_additional_6.map
AnnotationApoRNP Focused Refined (Right) Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ApoRNP Focused Refined (Right) Half Map B

Fileemd_26549_additional_7.map
AnnotationApoRNP Focused Refined (Right) Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ApoRNP Full Consensus Half Map A

Fileemd_26549_half_map_1.map
AnnotationApoRNP Full Consensus Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ApoRNP Full Consensus Half Map B

Fileemd_26549_half_map_2.map
AnnotationApoRNP Full Consensus Half Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of RNA and protein

EntireName: Complex of RNA and protein
Components
  • Complex: Complex of RNA and protein
    • RNA: E.r IIC Intron
    • Protein or peptide: Group II intron reverse transcriptase/maturase
  • Ligand: MAGNESIUM ION
  • Ligand: AMMONIUM ION

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Supramolecule #1: Complex of RNA and protein

SupramoleculeName: Complex of RNA and protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: E.r IIC Intron

MacromoleculeName: E.r IIC Intron / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 206.779859 KDa
SequenceString: GUUUGCGCGC CAUGGGCGCG CUCUAACGGG UGUAAGUCCC GAACAUGCCC AGGUAGUGGG AAAUGUAUAG CCGAACAGCA AGGGUGUCU ACUGUGAGGU GGAAUCUGAA GGAAGCUGUA AGCGAAUCUC UGGUCCGACG GACAGAAAUC GCAUAUAAGG C UAGGCUUC ...String:
GUUUGCGCGC CAUGGGCGCG CUCUAACGGG UGUAAGUCCC GAACAUGCCC AGGUAGUGGG AAAUGUAUAG CCGAACAGCA AGGGUGUCU ACUGUGAGGU GGAAUCUGAA GGAAGCUGUA AGCGAAUCUC UGGUCCGACG GACAGAAAUC GCAUAUAAGG C UAGGCUUC GAGUGAUAAG CUGGCAAAGA ACAGUGAAGU CUAAUAACUA CCACGUUUGU AGAAGCAGAG UAAAUGCGGC GG AUAUAUG GAGAGAAAGA GCGUGCACCU UAAGCGUGGA GGUCUCACAG AGGUUUCAUU AGCCUAGUAA CAACGAACUG UGA GAAGUC AGCCGAGCCC AUAGUAGUGA AGAAGUCUCU GUAAUGGGGA UGGAGCGAAG GGGCGAACAA UCAUUCAGUU UGAG AAUGU CUCGUAUUGC AGAAAUGACA ACAUCUGCCG UAACCAAUCG GGUAAAAGGU GGUCAAAUCA AGCGAGACGG AAAGG AAAG AACGCAUGGA CACAAGUAAU CUAAUUUCGG UUAGAUUACU ACAUCGAAAA GUGUGUUACU UGUUAAGUUG AUUGAA CCG CCGUAUACGG AACCGUACGU ACGGUGGUGU GAGAGGUCGG AAUUUCUCAA UUAAGAGAAA UUCUUCCUAC UCGAU

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Macromolecule #2: Group II intron reverse transcriptase/maturase

MacromoleculeName: Group II intron reverse transcriptase/maturase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 49.083914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDTSNLMEQI LSSDNLNRAY LQVVRNKGAE GVDGMKYTEL KEHLAKNGET IKGQLRTRKY KPQPARRVEI PKPDGGVRNL GVPTVTDRF IQQAIAQVLT PIYEEQFHDH SYGFRPNRCA QQAILTALNI MNDGNDWIVD IDLEKFFDTV NHDKLMTLIG R TIKDGDVI ...String:
MDTSNLMEQI LSSDNLNRAY LQVVRNKGAE GVDGMKYTEL KEHLAKNGET IKGQLRTRKY KPQPARRVEI PKPDGGVRNL GVPTVTDRF IQQAIAQVLT PIYEEQFHDH SYGFRPNRCA QQAILTALNI MNDGNDWIVD IDLEKFFDTV NHDKLMTLIG R TIKDGDVI SIVRKYLVSG IMIDDEYEDS IVGTPQGGNL SPLLANIMLN ELDKEMEKRG LNFVRYADDC IIMVGSEMSA NR VMRNISR FIEEKLGLKV NMTKSKVDRP SGLKYLGFGF YFDPRAHQFK AKPHAKSVAK FKKRMKELTC RSWGVSNSYK VEK LNQLIR GWINYFKIGS MKTLCKELDS RIRYRLRMCI WKQWKTPQNQ EKNLVKLGID RNTARRVAYT GKRIAYVCNK GAVN VAISN KRLASFGLIS MLDYYIEKCV TC

UniProtKB: Group II intron reverse transcriptase/maturase

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 13 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: AMMONIUM ION

MacromoleculeName: AMMONIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: NH4
Molecular weightTheoretical: 18.038 Da
Chemical component information

ChemComp-NH4:
AMMONIUM ION

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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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3eoh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 434467
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
FSC plot (resolution estimation)

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