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- PDB-9jp0: the wild-type human PRMT1 filament -

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Basic information

Entry
Database: PDB / ID: 9jp0
Titlethe wild-type human PRMT1 filament
ComponentsProtein arginine N-methyltransferase 1
KeywordsTRANSFERASE / Protein Arginine Methyltransferase / filament
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 / type I protein arginine methyltransferase / regulation of megakaryocyte differentiation / histone H3R8 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 / type I protein arginine methyltransferase / regulation of megakaryocyte differentiation / histone H3R8 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein methyltransferase activity / histone H3R17 methyltransferase activity / histone H3R26 methyltransferase activity / histone H4R3 methyltransferase activity / histone H3R2 methyltransferase activity / protein methylation / histone H2AQ104 methyltransferase activity / cellular response to methionine / protein-arginine N-methyltransferase activity / 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 / mitogen-activated protein kinase p38 binding / histone methyltransferase activity / negative regulation of megakaryocyte differentiation / positive regulation of double-strand break repair via homologous recombination / positive regulation of TORC1 signaling / RNA splicing / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of erythrocyte differentiation / 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 / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / 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
Protein arginine N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsLi, Y.W. / Ru, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentK22227503 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the human PRMT1 filament
Authors: Li, Y.W. / Ru, Y.X.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Protein arginine N-methyltransferase 1
B: Protein arginine N-methyltransferase 1
C: Protein arginine N-methyltransferase 1
F: Protein arginine N-methyltransferase 1
G: Protein arginine N-methyltransferase 1
H: Protein arginine N-methyltransferase 1
D: Protein arginine N-methyltransferase 1
A: Protein arginine N-methyltransferase 1
I: Protein arginine N-methyltransferase 1
J: Protein arginine N-methyltransferase 1


Theoretical massNumber of molelcules
Total (without water)425,11610
Polymers425,11610
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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: 42511.551 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT1, HMT2, HRMT1L2, IR1B4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99873, type I protein arginine methyltransferase
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: the wild type PRMT1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
8PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150914 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00425915
ELECTRON MICROSCOPYf_angle_d0.61935089
ELECTRON MICROSCOPYf_dihedral_angle_d15.7619514
ELECTRON MICROSCOPYf_chiral_restr0.0483929
ELECTRON MICROSCOPYf_plane_restr0.0034406

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