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- EMDB-38091: PRMT5:MEP50 WITH SCR-6920 AND SAM -

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Basic information

Entry
Database: EMDB / ID: EMD-38091
TitlePRMT5:MEP50 WITH SCR-6920 AND SAM
Map data
Sample
  • Complex: Ternary Complex of PRMT5:MEP50 WITH SCR-6920 AND SAM binding
    • Protein or peptide: Protein arginine N-methyltransferase 5
    • Protein or peptide: Methylosome protein WDR77
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: GLYCEROL
  • Ligand: 1-ethyl-8-[(2-methoxy-7-azaspiro[3.5]nonan-7-yl)carbonyl]-4-[2-oxidanylidene-2-[(3~{S})-1,2,3,4-tetrahydroisoquinolin-3-yl]ethyl]-2,3-dihydro-1,4-benzodiazepin-5-one
KeywordsCELL CYCLE / Cancer
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 H4R3 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 H4R3 methyltransferase activity / : / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / histone methyltransferase activity / regulation of mitotic nuclear division / negative regulation of gene expression via chromosomal CpG island methylation / Cul4B-RING E3 ubiquitin ligase complex / E-box binding / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / ubiquitin-like ligase-substrate adaptor activity / liver regeneration / regulation of signal transduction by p53 class mediator / methyltransferase activity / circadian regulation of gene expression / DNA-templated transcription termination / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / p53 binding / transcription corepressor activity / snRNP Assembly / ubiquitin-dependent protein catabolic process / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / 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. ...: / 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. / 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
Similarity search - Domain/homology
Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsZhou F
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: PRMT5:MEP50 WITH SCR-6920 AND SAM
Authors: Zhou F / Zhou F
History
DepositionNov 21, 2023-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38091.png

Downloads & links

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Map

FileDownload / File: emd_38091.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 295.4 Å		1.06 Å/pix.
x 280 pix.
= 295.4 Å		1.06 Å/pix.
x 280 pix.
= 295.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.144
Minimum - Maximum-0.712129 - 1.2095698
Average (Standard dev.)-0.0002279757 (±0.041263726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 295.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38091_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38091_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary Complex of PRMT5:MEP50 WITH SCR-6920 AND SAM binding

EntireName: Ternary Complex of PRMT5:MEP50 WITH SCR-6920 AND SAM binding
Components
  • Complex: Ternary Complex of PRMT5:MEP50 WITH SCR-6920 AND SAM binding
    • Protein or peptide: Protein arginine N-methyltransferase 5
    • Protein or peptide: Methylosome protein WDR77
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: GLYCEROL
  • Ligand: 1-ethyl-8-[(2-methoxy-7-azaspiro[3.5]nonan-7-yl)carbonyl]-4-[2-oxidanylidene-2-[(3~{S})-1,2,3,4-tetrahydroisoquinolin-3-yl]ethyl]-2,3-dihydro-1,4-benzodiazepin-5-one

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Supramolecule #1: Ternary Complex of PRMT5:MEP50 WITH SCR-6920 AND SAM binding

SupramoleculeName: Ternary Complex of PRMT5:MEP50 WITH SCR-6920 AND SAM binding
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.766664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.757246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Macromolecule #4: GLYCEROL

MacromoleculeName: GLYCEROL / type: ligand / ID: 4 / Number of copies: 4 / Formula: GOL
Molecular weightTheoretical: 92.094 Da
Chemical component information

ChemComp-GOL:
GLYCEROL

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Macromolecule #5: 1-ethyl-8-[(2-methoxy-7-azaspiro[3.5]nonan-7-yl)carbonyl]-4-[2-ox...

MacromoleculeName: 1-ethyl-8-[(2-methoxy-7-azaspiro[3.5]nonan-7-yl)carbonyl]-4-[2-oxidanylidene-2-[(3~{S})-1,2,3,4-tetrahydroisoquinolin-3-yl]ethyl]-2,3-dihydro-1,4-benzodiazepin-5-one
type: ligand / ID: 5 / Number of copies: 4 / Formula: YFU
Molecular weightTheoretical: 544.684 Da

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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

Concentration1.0 mg/mL
BufferpH: 7.4
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Alphafold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 804558
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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