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- EMDB-47477: Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47477
TitleCryo-EM structure of PRMT5/WDR77 in complex with 6S complex
Map dataMain map, unsharpened
Sample
  • Complex: PRMT5/WDR77 in complex with 6S
    • 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 ribonucleoprotein Sm D1
        • Protein or peptide: Small nuclear ribonucleoprotein Sm D1
      • Complex: Small nuclear ribonucleoproteins E, F, G
  • Ligand: SINEFUNGIN
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 / peptidyl-arginine methylation / protein-arginine omega-N symmetric methyltransferase activity / 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 / peptidyl-arginine methylation / protein-arginine omega-N symmetric methyltransferase activity / 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 H4R3 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / U12-type spliceosomal complex / histone H3K56 methyltransferase activity / 7-methylguanosine cap hypermethylation / protein-arginine N-methyltransferase activity / methylosome / U1 snRNP binding / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / small nuclear ribonucleoprotein complex / methyl-CpG binding / cell volume homeostasis / SMN-Sm protein complex / spliceosomal tri-snRNP complex / U2-type precatalytic spliceosome / histone H2A Q104 methyltransferase activity / U2-type spliceosomal complex / mRNA cis splicing, via spliceosome / commitment complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / chloride transport / U4 snRNP / endothelial cell activation / U2 snRNP / U1 snRNP / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase complex / precatalytic spliceosome / negative regulation of gene expression via chromosomal CpG island methylation / Cul4B-RING E3 ubiquitin ligase complex / histone methyltransferase activity / spliceosomal complex assembly / E-box binding / mRNA Splicing - Minor Pathway / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / U5 snRNP / ubiquitin-like ligase-substrate adaptor activity / regulation of ERK1 and ERK2 cascade / spliceosomal snRNP assembly / ribonucleoprotein complex binding / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / : / liver regeneration / regulation of signal transduction by p53 class mediator / methyltransferase activity / spliceosomal complex / circadian regulation of gene expression / DNA-templated transcription termination / mRNA splicing, via spliceosome / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / SARS-CoV-2 modulates host translation machinery / cytoskeleton / 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 / 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 / Small nuclear ribonucleoprotein D1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / 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 / 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 / Small nuclear ribonucleoprotein Sm D1 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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_47477.png

Downloads & links

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Map

FileDownload / File: emd_47477.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.11485323 - 0.29548496
Average (Standard dev.)0.000079616286 (±0.0070231827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47477_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map from cryoSPARC

Fileemd_47477_additional_1.map
Annotationsharpened map from cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_47477_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_47477_half_map_2.map
Annotationhalf map 2
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

EntireName: PRMT5/WDR77 in complex with 6S
Components
  • Complex: PRMT5/WDR77 in complex with 6S
    • 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 ribonucleoprotein Sm D1
        • Protein or peptide: Small nuclear ribonucleoprotein Sm D1
      • Complex: Small nuclear ribonucleoproteins E, F, G
  • Ligand: SINEFUNGIN

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Supramolecule #1: PRMT5/WDR77 in complex with 6S

SupramoleculeName: PRMT5/WDR77 in complex with 6S / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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-#4
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 ribonucleoprotein Sm D1

SupramoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: complex / ID: 5 / Parent: 3 / Macromolecule list: #4

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Supramolecule #6: Small nuclear ribonucleoproteins E, F, G

SupramoleculeName: Small nuclear ribonucleoproteins E, F, G / type: complex / ID: 6 / 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: 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 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: 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: 4 / 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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Macromolecule #4: Small nuclear ribonucleoprotein Sm D1

MacromoleculeName: Small nuclear ribonucleoprotein Sm D1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.954288 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GGGSGGGGRM KLVRFLMKLS HETVTIELKN GTQVHGTITG VDVSMNTHLK AVKMTLKNRE PVQLETLSIR GNNIRYFILP DSLPLDTLL VDVEPKVKSK KREAVAGRGR GRGRGRGRGR GRGRGGPRR

UniProtKB: Small nuclear ribonucleoprotein Sm D1

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Macromolecule #5: SINEFUNGIN

MacromoleculeName: SINEFUNGIN / type: ligand / ID: 5 / Number of copies: 4 / Formula: SFG
Molecular weightTheoretical: 381.387 Da
Chemical component information

ChemComp-SFG:
SINEFUNGIN

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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.9e-05 kPa
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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Details: as in cryosparc / Number images used: 377557
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 8
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: 110.5 / Target criteria: real space correlation
Output model

PDB-9e3b:
Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex

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