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- PDB-8z2z: PRMT1-Tetramer -

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Basic information

Entry
Database: PDB / ID: 8z2z
TitlePRMT1-Tetramer
ComponentsProtein arginine N-methyltransferase 1
KeywordsTRANSFERASE / tetramer
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 / methyl-CpG binding / positive regulation of p38MAPK cascade / 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 / cytosol / cytoplasm
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
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsEswarKumar, N. / Wang, C.H. / Ho, M.C.
Funding support Taiwan, 1items
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 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
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Revision 1.1Nov 12, 2025Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 1
B: Protein arginine N-methyltransferase 1
C: Protein arginine N-methyltransferase 1
D: Protein arginine N-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6778
Polymers153,1394
Non-polymers1,5384
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, We observed the complex in Cryo-EM structure.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Protein arginine N-methyltransferase 1 / Histone-arginine N-methyltransferase PRMT1 / Interferon receptor 1-bound protein 4


Mass: 38284.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT1, HMT2, HRMT1L2, IR1B4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q99873, type I protein arginine methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: PRMT1 / Type: CELL / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 100 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.25 Å / Resolution method: OTHER / Num. of particles: 32630 / Symmetry type: POINT

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