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- EMDB-39814: PRMT1-Decamer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-39814
TitlePRMT1-Decamer
Map data
Sample
  • Cell: PRMT1-Octamer
    • Protein or peptide: Protein arginine N-methyltransferase 1
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsPRMT1-Decamer / 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 / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / protein 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 / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / regulation of megakaryocyte differentiation / protein methyltransferase activity / protein methylation / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4K12 methyltransferase activity / histone H4R3 methyltransferase activity / cellular response to methionine / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / methylosome / S-adenosyl-L-methionine binding / negative regulation of JNK cascade / methyl-CpG binding / positive regulation of p38MAPK cascade / histone H2A Q104 methyltransferase activity / cardiac muscle tissue development / Maturation of nucleoprotein / mitogen-activated protein kinase p38 binding / histone methyltransferase activity / positive regulation of double-strand break repair via homologous recombination / negative regulation of megakaryocyte differentiation / 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 / 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 speciesEscherichia coli BL21(DE3) (bacteria) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsNadendla EK / Wang CH
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: PRMT1-Decamer
Authors: Nadendla EK / Wang CH
History
DepositionApr 20, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39814.png

Downloads & links

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Map

FileDownload / File: emd_39814.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2681979 - 2.4164882
Average (Standard dev.)0.0021639157 (±0.056291524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39814_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39814_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PRMT1-Octamer

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

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Supramolecule #1: PRMT1-Octamer

SupramoleculeName: PRMT1-Octamer / 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: 8 / 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: 8 / 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
Processinghelical reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 23.34 Å
Applied symmetry - Helical parameters - Δ&Phi: 103.59 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 541164
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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