[English] 日本語
Yorodumi
- PDB-9e3c: Cryo-EM structure of PRMT5/WDR77 in complex with 6S complex (GRG ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9e3c
TitleCryo-EM structure of PRMT5/WDR77 in complex with 6S complex (GRG local refine)
Components
  • Protein arginine N-methyltransferase 5
  • Small nuclear ribonucleoprotein Sm D1
KeywordsTRANSFERASE / PRMT5 / Methyl transferase / WDR77 / arginine
Function / homology
Function and homology information


positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / histone arginine N-methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / U12-type spliceosomal complex / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H4R3 methyltransferase activity / 7-methylguanosine cap hypermethylation / histone H3K56 methyltransferase activity / U1 snRNP binding / protein-arginine N-methyltransferase activity / methylosome / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / spliceosomal tri-snRNP complex / methyl-CpG binding / U2-type precatalytic spliceosome / U2-type spliceosomal complex / commitment complex / U2-type prespliceosome assembly / histone H2AQ104 methyltransferase activity / U2-type catalytic step 2 spliceosome / U4 snRNP / endothelial cell activation / U2 snRNP / U1 snRNP / histone H3 methyltransferase activity / regulation of mitotic nuclear division / precatalytic spliceosome / histone methyltransferase complex / negative regulation of gene expression via chromosomal CpG island methylation / 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 / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / 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 / transcription corepressor activity / p53 binding / snRNP Assembly / SARS-CoV-2 modulates host translation machinery / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / Golgi apparatus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 / Small nuclear ribonucleoprotein D1 / 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 / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
SINEFUNGIN / Protein arginine N-methyltransferase 5 / Small nuclear ribonucleoprotein Sm D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsJin, C.Y. / Hunkeler, M. / Fischer, E.S.
Funding support United States, 1items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
J: Protein arginine N-methyltransferase 5
M: Small nuclear ribonucleoprotein Sm D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1023
Polymers86,7212
Non-polymers3811
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
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.: 1
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 Small nuclear ribonucleoprotein Sm D1 / Sm-D1 / Sm-D autoantigen / snRNP core protein D1


Mass: 13954.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62314
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN
Sequence detailsThe precise residue numbers of the amino acid residues in chain M (snRNP Sm D1) cannot be ...The precise residue numbers of the amino acid residues in chain M (snRNP Sm D1) cannot be determined because of the number of GR repeats near the C-terminus of the protein. They are numbered as residues 109-114. However, this region could actually be 97-102, or any stretch of GRGRGR between residues 97 and 114.

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1PRMT5/WDR77 in complex with 6S (GRG active site local refine)COMPLEX#1-#20MULTIPLE SOURCES
2PRMT5/WDR77COMPLEX#11RECOMBINANT
36S complexCOMPLEX#21RECOMBINANT
4Methylosome subunit pIClnCOMPLEX3RECOMBINANT
5Small nuclear ribonucleoprotein Sm D1COMPLEX#23RECOMBINANT
6Small nuclear ribonucleoproteins E, F, GCOMPLEX3RECOMBINANT
Molecular weightValue: 0.77 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Details: 30 mM HEPES pH 7.4, 150 mM NaCl, 3 mM TCEP, 3.33 mM sinefungin
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
33 mMTCEPC9H15O6P1
43.33 mMsinefunginC15H23N7O51
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K

-
Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 53.112 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3615

-
Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEM4.1image acquisition
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraXmodel fitting
8ISOLDEmodel fitting
12cryoSPARC4.41classification
13cryoSPARC4.4.13D reconstruction
14PHENIX1.21.1_5286model refinement
15Coot0.9.6model refinement
Image processingDetails: motioncorrected on the fly by cryosparc live
CTF correctionDetails: as implemented in cryosparc live / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2100293 / Details: topaz
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 530317 / Symmetry type: POINT
Atomic model buildingB value: 110.3 / Protocol: OTHER / Space: REAL / Target criteria: real space correlation
Atomic model buildingPDB-ID: 6V0O

6v0o


Pdb chain-ID: A / Accession code: 6V0O / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 121.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00275226
ELECTRON MICROSCOPYf_angle_d0.52047106
ELECTRON MICROSCOPYf_chiral_restr0.042764
ELECTRON MICROSCOPYf_plane_restr0.0037929
ELECTRON MICROSCOPYf_dihedral_angle_d4.6018709

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more