+
Open data
-
Basic information
Entry | Database: PDB / ID: 6v0o | ||||||
---|---|---|---|---|---|---|---|
Title | PRMT5 bound to the PBM peptide from pICln | ||||||
![]() |
| ||||||
![]() | Transferase/Splicing / methylation / methyltransferase / epigenetic / SDMA / splicing / Transferase-Splicing complex | ||||||
Function / homology | ![]() positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity ...positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / histone arginine N-methyltransferase activity / histone H4R3 methyltransferase activity / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / pICln-Sm protein complex / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / cell volume homeostasis / mRNA cis splicing, via spliceosome / chloride transport / endothelial cell activation / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of gene expression via chromosomal CpG island methylation / E-box binding / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / regulation of ERK1 and ERK2 cascade / ribonucleoprotein complex binding / regulation of signal transduction by p53 class mediator / methyltransferase activity / liver regeneration / spliceosomal complex / circadian regulation of gene expression / DNA-templated transcription termination / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / cytoskeleton / transcription coactivator activity / cilium / chromatin remodeling / protein heterodimerization activity / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / Golgi apparatus / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | McMillan, B.J. / Raymond, D.D. | ||||||
![]() | ![]() Title: Molecular basis for substrate recruitment to the PRMT5 methylosome. Authors: Mulvaney, K.M. / Blomquist, C. / Acharya, N. / Li, R. / Ranaghan, M.J. / O'Keefe, M. / Rodriguez, D.J. / Young, M.J. / Kesar, D. / Pal, D. / Stokes, M. / Nelson, A.J. / Jain, S.S. / Yang, A. ...Authors: Mulvaney, K.M. / Blomquist, C. / Acharya, N. / Li, R. / Ranaghan, M.J. / O'Keefe, M. / Rodriguez, D.J. / Young, M.J. / Kesar, D. / Pal, D. / Stokes, M. / Nelson, A.J. / Jain, S.S. / Yang, A. / Mullin-Bernstein, Z. / Columbus, J. / Bozal, F.K. / Skepner, A. / Raymond, D. / LaRussa, S. / McKinney, D.C. / Freyzon, Y. / Baidi, Y. / Porter, D. / Aguirre, A.J. / Ianari, A. / McMillan, B. / Sellers, W.R. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 203.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 157.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 329.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 329.3 KB | Display | |
Data in XML | ![]() | 1.3 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6v0nC ![]() 4gqbS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 72766.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O14744, type II protein arginine methyltransferase |
---|---|
#2: Protein | Mass: 36723.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1404.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Chemical | ChemComp-SFG / |
#5: Chemical | ChemComp-ACE / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.5 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 30% PEG 3350 200 mM ammonium sulfate 0.05% w/v dodecyl-maltoside |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→44.94 Å / Num. obs: 28182 / % possible obs: 98.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 112.67 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.13 / Net I/σ(I): 8.37 |
Reflection shell | Resolution: 2.86→2.88 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.62 / Num. unique obs: 564 / CC1/2: 0.481 / Rrim(I) all: 2.02 / % possible all: 97.1 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4GQB Resolution: 2.86→44.94 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.88 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.356
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 209.33 Å2 / Biso mean: 115.75 Å2 / Biso min: 72.55 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.57 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.86→44.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.86→2.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
|