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- EMDB-47476: Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (pICl... -

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Basic information

Entry
Database: EMDB / ID: EMD-47476
TitleCryo-EM structure of PRMT5/WDR77 in complex with 6S complex (pICln PBM local refinement)
Map dataMap of locally refined PRMT5/WDR77/pICln PBM peptide
Sample
  • Complex: PRMT5/WDR77 in complex with 6S (PBM local refinement)
    • Complex: PRMT5/WDR77
      • Protein or peptide: Protein arginine N-methyltransferase 5
      • Protein or peptide: Methylosome protein WDR77
    • Complex: 6S complex
      • Complex: Methylosome subunit pICln
        • Protein or peptide: Methylosome subunit pICln
      • Complex: small nuclear ribonucleoproteins Sm D1, E, F, G
KeywordsPRMT5 / Methyl transferase / WDR77 / arginine / TRANSFERASE
Function / homology
Function and homology information


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 / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity ...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 / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity / epithelial cell proliferation involved in prostate gland development / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / methylosome / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / cell volume homeostasis / methyl-CpG binding / mRNA cis splicing, via spliceosome / histone H2AQ104 methyltransferase activity / chloride transport / endothelial cell activation / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of gene expression via chromosomal CpG island methylation / histone methyltransferase activity / E-box binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / liver regeneration / regulation of signal transduction by p53 class mediator / methyltransferase activity / spliceosomal complex / circadian regulation of gene expression / DNA-templated transcription termination / 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 / transcription coactivator activity / cilium / chromatin remodeling / protein heterodimerization activity / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / Golgi apparatus / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / PH-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 5 / Methylosome subunit pICln / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsJin CY / Hunkeler M / Fischer ES
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA262188 United States
CitationJournal: J Biol Chem / Year: 2025
Title: Substrate adaptors are flexible tethering modules that enhance substrate methylation by the arginine methyltransferase PRMT5.
Authors: Cyrus Y Jin / Moritz Hunkeler / Kathleen M Mulvaney / William R Sellers / Eric S Fischer /
Abstract: Protein arginine methyltransferase (PRMT) 5 is an essential arginine methyltransferase responsible for the majority of cellular symmetric dimethyl-arginine marks. PRMT5 uses substrate adaptors such ...Protein arginine methyltransferase (PRMT) 5 is an essential arginine methyltransferase responsible for the majority of cellular symmetric dimethyl-arginine marks. PRMT5 uses substrate adaptors such as pICln, RIOK1, and COPR5 to recruit and methylate a wide range of substrates. Although the substrate adaptors play important roles in substrate recognition, how they direct PRMT5 activity towards specific substrates remains incompletely understood. Using biochemistry and cryogenic electron microscopy, we show that these adaptors compete for the same binding site on PRMT5. We find that substrate adaptor and substrate complexes are bound to PRMT5 through two peptide motifs, enabling these adaptors to act as flexible tethering modules to enhance substrate methylation. Taken together, our results shed structural and mechanistic light on the PRMT5 substrate adaptor function and the biochemical nature of PRMT5 interactors.
History
DepositionOct 23, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47476.png

Downloads & links

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Map

FileDownload / File: emd_47476.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of locally refined PRMT5/WDR77/pICln PBM peptide
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 300 pix.
= 422.4 Å		1.41 Å/pix.
x 300 pix.
= 422.4 Å		1.41 Å/pix.
x 300 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.408 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.9634117 - 1.8082377
Average (Standard dev.)-0.0009764499 (±0.023826383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47476_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of local refinement of PRMT5/WDR77/pICln PBM peptide

Fileemd_47476_half_map_1.map
AnnotationHalf map of local refinement of PRMT5/WDR77/pICln PBM peptide
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of local refinement of PRMT5/WDR77/pICln PBM peptide

Fileemd_47476_half_map_2.map
AnnotationHalf map of local refinement of PRMT5/WDR77/pICln PBM peptide
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PRMT5/WDR77 in complex with 6S (PBM local refinement)

EntireName: PRMT5/WDR77 in complex with 6S (PBM local refinement)
Components
  • Complex: PRMT5/WDR77 in complex with 6S (PBM local refinement)
    • Complex: PRMT5/WDR77
      • Protein or peptide: Protein arginine N-methyltransferase 5
      • Protein or peptide: Methylosome protein WDR77
    • Complex: 6S complex
      • Complex: Methylosome subunit pICln
        • Protein or peptide: Methylosome subunit pICln
      • Complex: small nuclear ribonucleoproteins Sm D1, E, F, G

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Supramolecule #1: PRMT5/WDR77 in complex with 6S (PBM local refinement)

SupramoleculeName: PRMT5/WDR77 in complex with 6S (PBM local refinement) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 770 KDa

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Supramolecule #2: PRMT5/WDR77

SupramoleculeName: PRMT5/WDR77 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 6S complex

SupramoleculeName: 6S complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Methylosome subunit pICln

SupramoleculeName: Methylosome subunit pICln / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #3

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Supramolecule #5: small nuclear ribonucleoproteins Sm D1, E, F, G

SupramoleculeName: small nuclear ribonucleoproteins Sm D1, E, F, G / type: complex / ID: 5 / Parent: 3

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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: 1 / 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 WDR77

MacromoleculeName: Methylosome protein WDR77 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.186695 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGGRTMRKET PPPLVPPAAR EWNLPPNAPA CMERQLEAAR YRSDGALLLG ASSLSGRCWA GSLWLFKDPC AAPNEGFCSA GVQTEAGVA DLTWVGERGI LVASDSGAVE LWELDENETL IVSKFCKYEH DDIVSTVSVL SSGTQAVSGS KDICIKVWDL A QQVVLSSY ...String:
GGGRTMRKET PPPLVPPAAR EWNLPPNAPA CMERQLEAAR YRSDGALLLG ASSLSGRCWA GSLWLFKDPC AAPNEGFCSA GVQTEAGVA DLTWVGERGI LVASDSGAVE LWELDENETL IVSKFCKYEH DDIVSTVSVL SSGTQAVSGS KDICIKVWDL A QQVVLSSY RAHAAQVTCV AASPHKDSVF LSCSEDNRIL LWDTRCPKPA SQIGCSAPGY LPTSLAWHPQ QSEVFVFGDE NG TVSLVDT KSTSCVLSSA VHSQCVTGLV FSPHSVPFLA SLSEDCSLAV LDSSLSELFR SQAHRDFVRD ATWSPLNHSL LTT VGWDHQ VVHHVVPTEP LPAPGPASVT E

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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.552504 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SSGSMSFLKS FPPPGPAEGL LRQQPDTEAV LNGKGLGTGT LYIAESRLSW LDGSGLGFSL EYPTISLHAL SRDRSDCLGE HLYVMVNAK FEEESKEPVA DEEEEDSDDD VEPITEFRFV PSDKSALEAM FTAMCECQAL HPDPEDEDSD DYDGEEYDVE A HEQGQGDI ...String:
SSGSMSFLKS FPPPGPAEGL LRQQPDTEAV LNGKGLGTGT LYIAESRLSW LDGSGLGFSL EYPTISLHAL SRDRSDCLGE HLYVMVNAK FEEESKEPVA DEEEEDSDDD VEPITEFRFV PSDKSALEAM FTAMCECQAL HPDPEDEDSD DYDGEEYDVE A HEQGQGDI PTFYTYEEGL SHLTAEGQAT LERLEGMLSQ SVSSQYNMAG VRTEDSIRDY EDGMEVDTTP TVAGQFEDAD VD H

UniProtKB: Methylosome subunit pICln

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
30.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
3.0 mMC9H15O6PTCEP
3.33 mMC15H23N7O5sinefungin

Details: 30 mM HEPES pH 7.4, 150 mM NaCl, 3 mM TCEP, 3.33 mM sinefungin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3615 / Average exposure time: 5.0 sec. / Average electron dose: 53.112 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Detailsmotioncorrected on the fly by cryosparc live
Particle selectionNumber selected: 2100293 / Details: topaz
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 285661
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 8 / Software - Name: cryoSPARC (ver. 4.41)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6v0o

chain_id: A, source_name: PDB, initial_model_type: experimental model

6v0o

chain_id: B, source_name: PDB, initial_model_type: experimental model

6v0o

chain_id: C, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 98.6 / Target criteria: real space correlation
Output model

PDB-9e3a:
Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (pICln PBM local refinement)

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