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- EMDB-61691: the wild-type human PRMT1 filament -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61691
Titlethe wild-type human PRMT1 filament
Map datamap
Sample
  • Complex: the wild type PRMT1
    • Protein or peptide: Protein arginine N-methyltransferase 1
KeywordsProtein Arginine Methyltransferase / filament / TRANSFERASE
Function / homology
Function and homology information


GATOR1 complex binding / histone H3R8 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / positive regulation of hemoglobin biosynthetic process / histone H3R26 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / histone H3R17 methyltransferase activity ...GATOR1 complex binding / histone H3R8 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / positive regulation of hemoglobin biosynthetic process / histone H3R26 methyltransferase activity / protein-arginine omega-N monomethyltransferase activity / N-methyltransferase activity / histone H3R17 methyltransferase activity / peptidyl-arginine methylation / regulation of BMP signaling pathway / histone H2AQ104 methyltransferase activity / histone H3R2 methyltransferase activity / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsLi YW / Ru YX
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentK22227503 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the human PRMT1 filament
Authors: Li YW / Ru YX
History
DepositionSep 25, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61691.png

Downloads & links

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Map

FileDownload / File: emd_61691.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å		0.92 Å/pix.
x 200 pix.
= 184. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0132
Minimum - Maximum-0.03489984 - 0.067313746
Average (Standard dev.)0.0004906775 (±0.004904628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 184.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 2

Fileemd_61691_half_map_1.map
Annotation2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 1

Fileemd_61691_half_map_2.map
Annotation1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : the wild type PRMT1

EntireName: the wild type PRMT1
Components
  • Complex: the wild type PRMT1
    • Protein or peptide: Protein arginine N-methyltransferase 1

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Supramolecule #1: the wild type PRMT1

SupramoleculeName: the wild type PRMT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 10 / Enantiomer: LEVO / EC number: type I protein arginine methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.511551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAAEAANCI MENFVATLAN GMSLQPPLEE VSCGQAESSE KPNAEDMTSK DYYFDSYAHF GIHEEMLKDE VRTLTYRNSM FHNRHLFKD KVVLDVGSGT GILCMFAAKA GARKVIGIEC SSISDYAVKI VKANKLDHVV TIIKGKVEEV ELPVEKVDII I SEWMGYCL ...String:
MAAAEAANCI MENFVATLAN GMSLQPPLEE VSCGQAESSE KPNAEDMTSK DYYFDSYAHF GIHEEMLKDE VRTLTYRNSM FHNRHLFKD KVVLDVGSGT GILCMFAAKA GARKVIGIEC SSISDYAVKI VKANKLDHVV TIIKGKVEEV ELPVEKVDII I SEWMGYCL FYESMLNTVL YARDKWLAPD GLIFPDRATL YVTAIEDRQY KDYKIHWWEN VYGFDMSCIK DVAIKEPLVD VV DPKQLVT NACLIKEVDI YTVKVEDLTF TSPFCLQVKR NDYVHALVAY FNIEFTRCHK RTGFSTSPES PYTHWKQTVF YME DYLTVK TGEEIFGTIG MRPNAKNNRD LDFTIDLDFK GQLCELSCST DYRMR

UniProtKB: Protein arginine N-methyltransferase 1

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 150914
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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