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- EMDB-39821: PRMT1-Filament -

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Basic information

Entry
Database: EMDB / ID: EMD-39821
TitlePRMT1-Filament
Map data
Sample
  • Cell: PRMT1-Filament
    • Protein or peptide: Protein arginine N-methyltransferase 1
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsPRMT1-Filament / TRANSFERASE
Function / homology
Function and homology information


GATOR1 complex binding / positive regulation of hemoglobin biosynthetic process / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / peptidyl-arginine methylation / regulation of BMP signaling pathway / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity ...GATOR1 complex binding / positive regulation of hemoglobin biosynthetic process / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / peptidyl-arginine methylation / regulation of BMP signaling pathway / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / type I protein arginine methyltransferase / histone H4R3 methyltransferase activity / protein methyltransferase activity / protein methylation / protein-arginine N-methyltransferase activity / cellular response to methionine / methylosome / S-adenosyl-L-methionine binding / positive regulation of p38MAPK cascade / methyl-CpG binding / cardiac muscle tissue development / negative regulation of JNK cascade / Maturation of nucleoprotein / histone methyltransferase activity / mitogen-activated protein kinase p38 binding / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / positive regulation of TORC1 signaling / RNA splicing / positive regulation of erythrocyte differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of translation / methyltransferase activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / protein homooligomerization / RMTs methylate histone arginines / neuron projection development / Estrogen-dependent gene expression / in utero embryonic development / cell surface receptor signaling pathway / Extra-nuclear estrogen signaling / viral protein processing / chromatin remodeling / lysosomal membrane / positive regulation of cell population proliferation / DNA damage response / regulation of DNA-templated transcription / enzyme binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Arginine methyltransferase oligomerization subdomain / Methyltransferase domain 25 / Methyltransferase domain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Protein arginine N-methyltransferase 1
Similarity search - Component
Biological speciesEscherichia coli BL21(DE3) (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsEswarKumar N / Wang CH
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J Biol Chem / Year: 2024
Title: Oligomerization of protein arginine methyltransferase 1 and its functional impact on substrate arginine methylation.
Authors: Tran Dang / Nadendla EswarKumar / Sunil Kumar Tripathi / Chunli Yan / Chun-Hsiung Wang / Mengtong Cao / Tanmoy Kumar Paul / Elizabeth Oladoyin Agboluaje / May P Xiong / Ivaylo Ivanov / Meng- ...Authors: Tran Dang / Nadendla EswarKumar / Sunil Kumar Tripathi / Chunli Yan / Chun-Hsiung Wang / Mengtong Cao / Tanmoy Kumar Paul / Elizabeth Oladoyin Agboluaje / May P Xiong / Ivaylo Ivanov / Meng-Chiao Ho / Y George Zheng /
Abstract: Protein arginine methyltransferases (PRMTs) are important posttranslational modifying enzymes in eukaryotic proteins and regulate diverse pathways from gene transcription, RNA splicing, and signal ...Protein arginine methyltransferases (PRMTs) are important posttranslational modifying enzymes in eukaryotic proteins and regulate diverse pathways from gene transcription, RNA splicing, and signal transduction to metabolism. Increasing evidence supports that PRMTs exhibit the capacity to form higher-order oligomeric structures, but the structural basis of PRMT oligomerization and its functional consequence are elusive. Herein, we revealed for the first time different oligomeric structural forms of the predominant arginine methyltransferase PRMT1 using cryo-EM, which included tetramer (dimer of dimers), hexamer (trimer of dimers), octamer (tetramer of dimers), decamer (pentamer of dimers), and also helical filaments. Through a host of biochemical assays, we showed that PRMT1 methyltransferase activity was substantially enhanced as a result of the high-ordered oligomerization. High-ordered oligomerization increased the catalytic turnover and the multimethylation processivity of PRMT1. Presence of a catalytically dead PRMT1 mutant also enhanced the activity of WT PRMT1, pointing out a noncatalytic role of oligomerization. Structural modeling demonstrates that oligomerization enhances substrate retention at the PRMT1 surface through electrostatic force. Our studies offered key insights into PRMT1 oligomerization and established that oligomerization constitutes a novel molecular mechanism that positively regulates the enzymatic activity of PRMTs in biology.
History
DepositionApr 20, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39821.png

Downloads & links

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Map

FileDownload / File: emd_39821.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.8476121 - 6.063524
Average (Standard dev.)-0.001227456 (±0.18648243)
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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Half map: #1

Fileemd_39821_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_39821_half_map_2.map
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Sample components

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Entire : PRMT1-Filament

EntireName: PRMT1-Filament
Components
  • Cell: PRMT1-Filament
    • Protein or peptide: Protein arginine N-methyltransferase 1
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: PRMT1-Filament

SupramoleculeName: PRMT1-Filament / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: Protein arginine N-methyltransferase 1

MacromoleculeName: Protein arginine N-methyltransferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: type I protein arginine methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.284848 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: PNAEDMTSKD YYFDSYAHFG IHEEMLKDEV RTLTYRNSMF HNRHLFKDKV VLDVGSGTGI LCMFAAKAGA RKVIGIECSS ISDYAVKIV KANKLDHVVT IIKGKVEEVE LPVEKVDIII SEWMGYCLFY ESMLNTVLYA RDKWLAPDGL IFPDRATLYV T AIEDRQYK ...String:
PNAEDMTSKD YYFDSYAHFG IHEEMLKDEV RTLTYRNSMF HNRHLFKDKV VLDVGSGTGI LCMFAAKAGA RKVIGIECSS ISDYAVKIV KANKLDHVVT IIKGKVEEVE LPVEKVDIII SEWMGYCLFY ESMLNTVLYA RDKWLAPDGL IFPDRATLYV T AIEDRQYK DYKIHWWENV YGFDMSCIKD VAIKEPLVDV VDPKQLVTNA CLIKEVDIYT VKVEDLTFTS PFCLQVKRND YV HALVAYF NIEFTRCHKR TGFSTSPESP YTHWKQTVFY MEDYLTVKTG EEIFGTIGMR PNAKNNRDLD FTIDLDFKGQ LCE LSCSTD YRMR

UniProtKB: Protein arginine N-methyltransferase 1

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Macromolecule #2: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 2 / Number of copies: 24 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 541349
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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