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- PDB-6rll: CRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ44064146 -

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Basic information

Entry
Database: PDB / ID: 6rll
TitleCRYSTAL STRUCTURE OF THE HUMAN PRMT5:MEP50 COMPLEX with JNJ44064146
Components
  • Methylosome protein 50
  • Protein arginine N-methyltransferase 5
KeywordsTRANSLOCASE / PRMT5 / MEP50 / LIGAND
Function / homology
Function and homology information


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 / epithelial cell proliferation involved in prostate gland development / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity / histone H3R26 methyltransferase activity / histone H3K37 methyltransferase activity / histone H4R3 methyltransferase activity / histone H4K12 methyltransferase activity / histone H3K56 methyltransferase activity / protein-arginine N-methyltransferase activity / methylosome / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / histone H2AQ104 methyltransferase activity / endothelial cell activation / histone H3 methyltransferase activity / regulation of mitotic nuclear division / histone methyltransferase complex / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of gene expression via chromosomal CpG island methylation / histone methyltransferase activity / E-box binding / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / liver regeneration / regulation of signal transduction by p53 class mediator / methyltransferase activity / 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 / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 ...: / Protein arginine N-methyltransferase PRMT5 / PRMT5, TIM barrel domain / PRMT5, oligomerisation domain / PRMT5 TIM barrel domain / PRMT5 oligomerisation domain / PRMT5 arginine-N-methyltransferase / PRMT5 arginine-N-methyltransferase / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Divalent-metal-dependent TIM barrel enzymes / YVTN repeat-like/Quinoprotein amine dehydrogenase / Vaccinia Virus protein VP39 / 7 Propeller / Methylamine Dehydrogenase; Chain H / Distorted Sandwich / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / WD40/YVTN repeat-like-containing domain superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-K8H / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsBrown, D.G. / Robinson, C.M. / Pande, V.
CitationJournal: To Be Published
Title: A chemical probe for the methyl transferase PRMT5 with a novel binding mode
Authors: Brown, D.G. / Robinson, C.M. / Pandeet, V.
History
DepositionMay 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 5
B: Methylosome protein 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7383
Polymers111,3502
Non-polymers3881
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-14 kcal/mol
Surface area36660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.956, 136.048, 179.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein arginine N-methyltransferase 5 / 72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / ...72 kDa ICln-binding protein / Histone-arginine N-methyltransferase PRMT5 / Jak-binding protein 1 / Shk1 kinase-binding protein 1 homolog / SKB1Hs


Mass: 73763.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein Methylosome protein 50 / MEP-50 / Androgen receptor cofactor p44 / WD repeat-containing protein 77 / p44/Mep50


Mass: 37586.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR77, MEP50, WD45, HKMT1069, Nbla10071
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9BQA1
#3: Chemical ChemComp-K8H / (2~{R},3~{R},4~{S},5~{R})-2-(4-azanylpyrrolo[2,3-d]pyrimidin-7-yl)-5-(1,8-diazaspiro[4.5]decan-1-ylmethyl)oxolane-3,4-diol


Mass: 388.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20-30% PEG3350; 150mM Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91739 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91739 Å / Relative weight: 1
ReflectionResolution: 2.22→89.65 Å / Num. obs: 60395 / % possible obs: 97.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 4 / Redundancy: 6.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.058 / Net I/σ(I): 13.5
Reflection shellResolution: 2.22→2.31 Å / Num. unique obs: 6070 / CC1/2: 0.85 / % possible all: 87.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GQB

4gqb


Resolution: 2.22→89.44 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.24
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2911 3002 5 %RANDOM
Rwork0.2508 ---
obs0.2529 57140 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.43 Å2 / Biso mean: 34.864 Å2 / Biso min: 18.44 Å2
Baniso -1Baniso -2Baniso -3
1-6.63 Å2-0 Å20 Å2
2---0.84 Å2-0 Å2
3----5.79 Å2
Refinement stepCycle: final / Resolution: 2.22→89.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 28 94 7400
Biso mean--25.46 54.44 -
Num. residues----928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137514
X-RAY DIFFRACTIONr_bond_other_d0.0360.0176712
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.63710255
X-RAY DIFFRACTIONr_angle_other_deg2.4831.56715584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2755926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46122.397388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.248151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1921544
X-RAY DIFFRACTIONr_chiral_restr0.0880.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028450
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021598
X-RAY DIFFRACTIONr_mcbond_it2.4193.713714
X-RAY DIFFRACTIONr_mcbond_other2.4193.7093713
X-RAY DIFFRACTIONr_mcangle_it3.8535.5554636
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 188 -
Rwork0.466 3626 -
all-3814 -
obs--83.86 %

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