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Open data
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Basic information
Entry | Database: PDB / ID: 8g1u | ||||||
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Title | Structure of the methylosome-Lsm10/11 complex | ||||||
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![]() | TRANSFERASE / Methylation / GENE REGULATION | ||||||
Function / homology | ![]() : / snRNP Assembly / mRNA 3'-end processing by stem-loop binding and cleavage / positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation ...: / snRNP Assembly / mRNA 3'-end processing by stem-loop binding and cleavage / positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / negative regulation of cell volume / histone H4R3 methyltransferase activity / regulation of chromatin organization / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / U7 snRNA binding / U7 snRNP / histone arginine N-methyltransferase activity / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / E-box binding / pICln-Sm protein complex / methyl-CpG binding / cell volume homeostasis / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / endothelial cell activation / histone H3 methyltransferase activity / chloride transport / positive regulation of mRNA splicing, via spliceosome / RNA Polymerase II Transcription Termination / negative regulation of gene expression via chromosomal CpG island methylation / regulation of mitotic nuclear division / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase complex / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / spliceosomal snRNP assembly / liver regeneration / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / DNA-templated transcription termination / spliceosomal complex / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / p53 binding / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / snRNP Assembly / ubiquitin-dependent protein catabolic process / chromatin remodeling / cytoskeleton / nuclear body / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å | ||||||
![]() | Lin, M. / Paige, A. / Tong, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome. Authors: Xiao-Cui Yang / Anthony Desotell / Min-Han Lin / Andrew S Paige / Agata Malinowska / Yadong Sun / Wei Shen Aik / Michał Dadlez / Liang Tong / Zbigniew Dominski / ![]() ![]() Abstract: U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 ...U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B, and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50, and pICln known to methylate arginines in the carboxy-terminal regions of the Sm proteins B, D1, and D3 during the spliceosomal Sm ring assembly. Both biochemical and cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the amino-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an amino-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 674.5 KB | Display | ![]() |
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PDB format | ![]() | 531.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 100.1 KB | Display | |
Data in CIF | ![]() | 153 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 29677MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 72766.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: O14744, type II protein arginine methyltransferase #2: Protein | Mass: 36757.246 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 26038.957 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 39572.793 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Chemical | ChemComp-ADN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Methylosome / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1250 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 58.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 754047 / Symmetry type: POINT | ||||||||||||||||||||||||
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