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- PDB-8g1u: Structure of the methylosome-Lsm10/11 complex -

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Basic information

Entry
Database: PDB / ID: 8g1u
TitleStructure of the methylosome-Lsm10/11 complex
Components
  • Methylosome protein 50
  • Methylosome subunit pICln
  • Protein arginine N-methyltransferase 5
  • U7 snRNA-associated Sm-like protein LSm11
KeywordsTRANSFERASE / Methylation / GENE REGULATION
Function / homology
Function and homology information


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 ...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 / regulation of chromatin organization / U7 snRNA binding / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / U7 snRNP / histone H4R3 methyltransferase activity / negative regulation of cell volume / : / 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 / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / telomerase holoenzyme complex / chloride transport / endothelial cell activation / RNA Polymerase II Transcription Termination / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of gene expression via chromosomal CpG island methylation / E-box binding / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / positive regulation of G1/S transition of mitotic cell cycle / spliceosomal snRNP assembly / regulation of ERK1 and ERK2 cascade / ribonucleoprotein complex binding / ubiquitin-like ligase-substrate adaptor activity / liver regeneration / regulation of signal transduction by p53 class mediator / methyltransferase activity / Regulation of TP53 Activity through Methylation / circadian regulation of gene expression / DNA-templated transcription termination / RMTs methylate histone arginines / protein polyubiquitination / p53 binding / transcription corepressor activity / snRNP Assembly / ubiquitin-dependent protein catabolic process / cytoskeleton / transcription coactivator activity / nuclear body / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / ICln / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / : / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain ...Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / ICln / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / : / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / Divalent-metal-dependent TIM barrel enzymes / : / Sm domain profile. / LSM domain superfamily / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / Protein arginine N-methyltransferase 5 / U7 snRNA-associated Sm-like protein LSm11 / Methylosome subunit pICln / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLin, M. / Paige, A. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: RNA / Year: 2023
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.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
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Revision 1.1Oct 25, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
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Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
C: Methylosome subunit pICln
E: Protein arginine N-methyltransferase 5
F: Methylosome protein 50
G: Methylosome subunit pICln
I: Protein arginine N-methyltransferase 5
J: Methylosome protein 50
K: Methylosome subunit pICln
M: Protein arginine N-methyltransferase 5
N: Methylosome protein 50
O: Methylosome subunit pICln
D: U7 snRNA-associated Sm-like protein LSm11
H: U7 snRNA-associated Sm-like protein LSm11
L: U7 snRNA-associated Sm-like protein LSm11
P: U7 snRNA-associated Sm-like protein LSm11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)701,61220
Polymers700,54316
Non-polymers1,0694
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Protein arginine N-methyltransferase 5 / 72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / ...72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / Shk1 kinase-binding protein 1 homolog / SKB1Hs


Mass: 72766.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein
Methylosome protein 50 / MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / p44/Mep50


Mass: 36757.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BQA1
#3: Protein
Methylosome subunit pICln / Chloride channel / nucleotide sensitive 1A / Chloride conductance regulatory protein ICln / I(Cln) ...Chloride channel / nucleotide sensitive 1A / Chloride conductance regulatory protein ICln / I(Cln) / Chloride ion current inducer protein / ClCI


Mass: 26038.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clns1a, Clci, Clcni / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q61189
#4: Protein
U7 snRNA-associated Sm-like protein LSm11


Mass: 39572.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSM11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P83369
#5: Chemical
ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Methylosome / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1250 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 58.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 754047 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00929873
ELECTRON MICROSCOPYf_angle_d0.86840632
ELECTRON MICROSCOPYf_dihedral_angle_d19.2883940
ELECTRON MICROSCOPYf_chiral_restr0.0574461
ELECTRON MICROSCOPYf_plane_restr0.0065268

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