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- EMDB-29677: Structure of the methylosome-Lsm10/11 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-29677
TitleStructure of the methylosome-Lsm10/11 complex
Map data
Sample
  • Complex: Methylosome
    • Protein or peptide: Protein arginine N-methyltransferase 5
    • Protein or peptide: Methylosome protein 50
    • Protein or peptide: Methylosome subunit pICln
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm11
  • Ligand: ADENOSINE
KeywordsMethylation / GENE REGULATION / TRANSFERASE
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 / peptidyl-arginine methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / 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 / peptidyl-arginine methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / regulation of chromatin organization / negative regulation of cell volume / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / U7 snRNA binding / histone arginine N-methyltransferase activity / U7 snRNP / 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 / methyl-CpG binding / telomerase holoenzyme complex / cell volume homeostasis / mRNA cis splicing, via spliceosome / endothelial cell activation / histone H3 methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / chloride transport / RNA Polymerase II Transcription Termination / regulation of mitotic nuclear division / histone methyltransferase complex / negative regulation of gene expression via chromosomal CpG island methylation / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / positive regulation of G1/S transition of mitotic cell cycle / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / liver regeneration / DNA-templated transcription termination / spliceosomal complex / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / cytoskeleton / nuclear body / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
ICln / Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / : / Protein arginine N-methyltransferase PRMT5 / PRMT5 arginine-N-methyltransferase / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain ...ICln / Sm-like protein Lsm11, middle domain / U7 snRNA-associated Sm-like protein Lsm11 / Protein ICln/Lot5/Saf5 / Regulator of volume decrease after cellular swelling / : / Protein arginine N-methyltransferase PRMT5 / PRMT5 arginine-N-methyltransferase / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / PH-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsLin M / Paige A / Tong L
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29677.png

Downloads & links

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Map

FileDownload / File: emd_29677.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 324 pix.
= 268.92 Å		0.83 Å/pix.
x 324 pix.
= 268.92 Å		0.83 Å/pix.
x 324 pix.
= 268.92 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-4.912006 - 6.752662
Average (Standard dev.)0.0030647742 (±0.23270018)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 268.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29677_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_29677_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Methylosome

EntireName: Methylosome
Components
  • Complex: Methylosome
    • Protein or peptide: Protein arginine N-methyltransferase 5
    • Protein or peptide: Methylosome protein 50
    • Protein or peptide: Methylosome subunit pICln
    • Protein or peptide: U7 snRNA-associated Sm-like protein LSm11
  • Ligand: ADENOSINE

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Supramolecule #1: Methylosome

SupramoleculeName: Methylosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Protein arginine N-methyltransferase 5

MacromoleculeName: Protein arginine N-methyltransferase 5 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: type II protein arginine methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.766664 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAMAVGGAG GSRVSSGRDL NCVPEIADTL GAVAKQGFDF LCMPVFHPRF KREFIQEPAK NRPGPQTRSD LLLSGRDWNT LIVGKLSPW IRPDSKVEKI RRNSEAAMLQ ELNFGAYLGL PAFLLPLNQE DNTNLARVLT NHIHTGHHSS MFWMRVPLVA P EDLRDDII ...String:
MAAMAVGGAG GSRVSSGRDL NCVPEIADTL GAVAKQGFDF LCMPVFHPRF KREFIQEPAK NRPGPQTRSD LLLSGRDWNT LIVGKLSPW IRPDSKVEKI RRNSEAAMLQ ELNFGAYLGL PAFLLPLNQE DNTNLARVLT NHIHTGHHSS MFWMRVPLVA P EDLRDDII ENAPTTHTEE YSGEEKTWMW WHNFRTLCDY SKRIAVALEI GADLPSNHVI DRWLGEPIKA AILPTSIFLT NK KGFPVLS KMHQRLIFRL LKLEVQFIIT GTNHHSEKEF CSYLQYLEYL SQNRPPPNAY ELFAKGYEDY LQSPLQPLMD NLE SQTYEV FEKDPIKYSQ YQQAIYKCLL DRVPEEEKDT NVQVLMVLGA GRGPLVNASL RAAKQADRRI KLYAVEKNPN AVVT LENWQ FEEWGSQVTV VSSDMREWVA PEKADIIVSE LLGSFADNEL SPECLDGAQH FLKDDGVSIP GEYTSFLAPI SSSKL YNEV RACREKDRDP EAQFEMPYVV RLHNFHQLSA PQPCFTFSHP NRDPMIDNNR YCTLEFPVEV NTVLHGFAGY FETVLY QDI TLSIRPETHS PGMFSWFPIL FPIKQPITVR EGQTICVRFW RCSNSKKVWY EWAVTAPVCS AIHNPTGRSY TIGL

UniProtKB: Protein arginine N-methyltransferase 5

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Macromolecule #2: Methylosome protein 50

MacromoleculeName: Methylosome protein 50 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.757246 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MRKETPPPLV PPAAREWNLP PNAPACMERQ LEAARYRSDG ALLLGASSLS GRCWAGSLWL FKDPCAAPNE GFCSAGVQTE AGVADLTWV GERGILVASD SGAVELWELD ENETLIVSKF CKYEHDDIVS TVSVLSSGTQ AVSGSKDICI KVWDLAQQVV L SSYRAHAA ...String:
MRKETPPPLV PPAAREWNLP PNAPACMERQ LEAARYRSDG ALLLGASSLS GRCWAGSLWL FKDPCAAPNE GFCSAGVQTE AGVADLTWV GERGILVASD SGAVELWELD ENETLIVSKF CKYEHDDIVS TVSVLSSGTQ AVSGSKDICI KVWDLAQQVV L SSYRAHAA QVTCVAASPH KDSVFLSCSE DNRILLWDTR CPKPASQIGC SAPGYLPTSL AWHPQQSEVF VFGDENGTVS LV DTKSTSC VLSSAVHSQC VTGLVFSPHS VPFLASLSED CSLAVLDSSL SELFRSQAHR DFVRDATWSP LNHSLLTTVG WDH QVVHHV VPTEPLPAPG PASVTE

UniProtKB: Methylosome protein WDR77

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Macromolecule #3: Methylosome subunit pICln

MacromoleculeName: Methylosome subunit pICln / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.038957 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSFLKSFPPP GSADGLRLQQ PDTEAVLNGK GLGTGTLYIA ESRLSWLDGS GLGFSLEYPT ISLHAVSRDP NAYPQEHLYV MVNAKLGEE SKEPPSDEDE EDNDDIEPIS EFRFVPSDKS ALEAMFTAMC ECQALHPDPE DEDSDDYDGE EYDVEAHEQG Q GDIPTFYT ...String:
MSFLKSFPPP GSADGLRLQQ PDTEAVLNGK GLGTGTLYIA ESRLSWLDGS GLGFSLEYPT ISLHAVSRDP NAYPQEHLYV MVNAKLGEE SKEPPSDEDE EDNDDIEPIS EFRFVPSDKS ALEAMFTAMC ECQALHPDPE DEDSDDYDGE EYDVEAHEQG Q GDIPTFYT YEEGLSHLTA EGQATLERLE GMLSQSVSSQ YNMAGVRTED SVRNYEDGME VETTPTVAGQ FEDADVDH

UniProtKB: Methylosome subunit pICln

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Macromolecule #4: U7 snRNA-associated Sm-like protein LSm11

MacromoleculeName: U7 snRNA-associated Sm-like protein LSm11 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.572793 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEERERGARS AGAGSPARPP SPRLDVSSDS FDPLLALYAP RLPPIPYPNA PCFNNVAEYE SFLRTGVRGG GRGRGRARGA AAGSGVPAA PGPSGRTRRR PDAPAPDPER IQRLRRLMVA KEEGDGAAGA GRRGPGRSRK APRNVLTRMP LHEGSPLGEL H RCIREGVK ...String:
MEERERGARS AGAGSPARPP SPRLDVSSDS FDPLLALYAP RLPPIPYPNA PCFNNVAEYE SFLRTGVRGG GRGRGRARGA AAGSGVPAA PGPSGRTRRR PDAPAPDPER IQRLRRLMVA KEEGDGAAGA GRRGPGRSRK APRNVLTRMP LHEGSPLGEL H RCIREGVK VNVHIRTFKG LRGVCTGFLV AFDKFWNMAL TDVDETYRKP VLGKAYERDS SLTLTRLFDR LKLQDSSKKE AD SKSAVED STLSRYSQTS TWKLASVWGR ADTGRGSHKR SRSVPSSLQA SAREESRSEL SGRTTRTDGS SVGGTFSRAT TLS RGQSRK KKRKPKVDYQ QVFTRHINQI FIRGENVLLV HLAQ

UniProtKB: U7 snRNA-associated Sm-like protein LSm11

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Macromolecule #5: ADENOSINE

MacromoleculeName: ADENOSINE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ADN
Molecular weightTheoretical: 267.241 Da
Chemical component information

ChemComp-ADN:
ADENOSINE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.25 µm / Nominal defocus min: 0.8 µm
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:

6v0o

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 754047
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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