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Yorodumi- EMDB-40985: Structure of a group II intron ribonucleoprotein in the pre-ligat... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40985 | |||||||||
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Title | Structure of a group II intron ribonucleoprotein in the pre-ligation (pre-2F) state | |||||||||
Map data | Overall Reconstruction of Pre-2F | |||||||||
Sample |
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Keywords | RNP / RNA / Transferase-RNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | [Eubacterium] rectale (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Xu L / Liu T / Chung K / Pyle AM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2023 Title: Structural insights into intron catalysis and dynamics during splicing. Authors: Ling Xu / Tianshuo Liu / Kevin Chung / Anna Marie Pyle / Abstract: The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns. Despite the importance of ...The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns. Despite the importance of branching in RNA metabolism, structural understanding of this process has remained elusive. Here we present a comprehensive analysis of three single-particle cryogenic electron microscopy structures captured along the splicing pathway. They reveal the network of molecular interactions that specifies the branchpoint adenosine and positions key functional groups to catalyse lariat formation and coordinate exon ligation. The structures also reveal conformational rearrangements of the branch helix and the mechanism of splice site exchange that facilitate the transition from branching to ligation. These findings shed light on the evolution of splicing and highlight the conservation of structural components, catalytic mechanism and dynamical strategies retained through time in premessenger RNA splicing machines. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40985.map.gz | 204 MB | EMDB map data format | |
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Header (meta data) | emd-40985-v30.xml emd-40985.xml | 20.9 KB 20.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40985_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_40985.png | 60.7 KB | ||
Masks | emd_40985_msk_1.map emd_40985_msk_2.map | 216 MB 216 MB | Mask map | |
Filedesc metadata | emd-40985.cif.gz | 6.2 KB | ||
Others | emd_40985_additional_1.map.gz emd_40985_additional_2.map.gz emd_40985_half_map_1.map.gz emd_40985_half_map_2.map.gz | 203.8 MB 203.9 MB 200.6 MB 200.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40985 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40985 | HTTPS FTP |
-Related structure data
Related structure data | 8t2rMC 8t2sC 8t2tC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40985.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Overall Reconstruction of Pre-2F | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.844 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40985_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_40985_msk_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Locally Refined (Left) Reconstruction of Pre-2F
File | emd_40985_additional_1.map | ||||||||||||
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Annotation | Locally Refined (Left) Reconstruction of Pre-2F | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Locally Refined (Right) Reconstruction of Pre-2F
File | emd_40985_additional_2.map | ||||||||||||
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Annotation | Locally Refined (Right) Reconstruction of Pre-2F | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall Reconstruction of Pre-2F Half Map A
File | emd_40985_half_map_1.map | ||||||||||||
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Annotation | Overall Reconstruction of Pre-2F Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall Reconstruction of Pre-2F Half Map B
File | emd_40985_half_map_2.map | ||||||||||||
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Annotation | Overall Reconstruction of Pre-2F Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Intron RNP complex in pre-2f
Entire | Name: Intron RNP complex in pre-2f |
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Components |
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-Supramolecule #1: Intron RNP complex in pre-2f
Supramolecule | Name: Intron RNP complex in pre-2f / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: [Eubacterium] rectale (bacteria) |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Group II intron reverse transcriptase/maturase
Macromolecule | Name: Group II intron reverse transcriptase/maturase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase |
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Source (natural) | Organism: [Eubacterium] rectale (bacteria) |
Molecular weight | Theoretical: 49.083914 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: 5'exon
Macromolecule | Name: 5'exon / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: [Eubacterium] rectale (bacteria) |
Molecular weight | Theoretical: 2.097219 KDa |
Sequence | String: UUUCUUU |
-Macromolecule #3: Intron
Macromolecule | Name: Intron / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: [Eubacterium] rectale (bacteria) |
Molecular weight | Theoretical: 208.395812 KDa |
Sequence | String: 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 UCAAUCAGUU UGAG UAUGU 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 UCGAUUG AA U |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 13 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: AMMONIUM ION
Macromolecule | Name: AMMONIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: NH4 |
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Molecular weight | Theoretical: 18.038 Da |
Chemical component information | ChemComp-NH4: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |