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- PDB-9pca: HUMAN PRMT5:MEP50 COMPLEX IN COMPLEX WITH LIGAND 18 -

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Basic information

Entry
Database: PDB / ID: 9pca
TitleHUMAN PRMT5:MEP50 COMPLEX IN COMPLEX WITH LIGAND 18
Components
  • Methylosome protein WDR77
  • 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 H4R3 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 H4R3 methyltransferase activity / : / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / positive regulation of mRNA splicing, via spliceosome / methyl-CpG binding / endothelial cell activation / histone H3 methyltransferase activity / histone methyltransferase activity / regulation of mitotic nuclear division / negative regulation of gene expression via chromosomal CpG island methylation / Cul4B-RING E3 ubiquitin ligase complex / E-box binding / histone methyltransferase complex / positive regulation of oligodendrocyte differentiation / negative regulation of cell differentiation / spliceosomal snRNP assembly / ribonucleoprotein complex binding / regulation of ERK1 and ERK2 cascade / ubiquitin-like ligase-substrate adaptor activity / 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 / p53 binding / transcription corepressor activity / 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 / cytoplasm / cytosol
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 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. ...: / 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 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / Protein arginine N-methyltransferase 5 / Methylosome protein WDR77
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMilligan, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Gut-Restricted PRMT5 Inhibitors to Intercept Colorectal Cancer in Patients with Genetic Loss of Tumor Suppressor Adenomatous Polyposis Coli.
Authors: Hulpia, F. / Schepens, W. / Lepri, S. / Nicolai, J. / Jiang, Z. / Boj, S.F. / Bush, T.L. / Carvalho, M.A. / Chen, F. / Chu, G. / Clancy, K.W. / Etwebi, Z. / Everaerts, M. / Fan, Y. / ...Authors: Hulpia, F. / Schepens, W. / Lepri, S. / Nicolai, J. / Jiang, Z. / Boj, S.F. / Bush, T.L. / Carvalho, M.A. / Chen, F. / Chu, G. / Clancy, K.W. / Etwebi, Z. / Everaerts, M. / Fan, Y. / Fernandez Candelaria, F.O. / Francis, A. / Hixon, M.S. / Jardi, F. / Jin, S. / Larin, E.M. / Last, S. / Leenaerts, J.E. / Li, S. / Liddane, A.G. / Lutter, F.H. / Lv, D. / Mattson, B. / Milligan, C.M. / Patrick, A.N. / Patwardhan, G.A. / Perez-Benito, L. / Pieters, S. / Renders, E. / Retzbach, E. / Smith-Monroy, C. / Silva, J. / Silva, M. / Sterckx, H. / Ten Hag, G. / Thate, C. / Van Brandt, S. / Verissimo, C.S. / Verniest, G. / Vesely, E. / Vetrano, I. / Vinken, P. / Wang, Y. / Wong, V. / Yao, X. / Yang, J. / Zijlmans, R. / Bachman, K.E. / Pocalyko, D. / Jimenez, J.M. / Gaffney, D. / Thuring, J.W.
History
DepositionJun 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine N-methyltransferase 5
B: Methylosome protein WDR77
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,31011
Polymers111,3502
Non-polymers9609
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.807, 139.139, 179.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 2 types, 2 molecules AB

#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 / Fragment: FULL LENGTH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14744, type II protein arginine methyltransferase
#2: Protein Methylosome protein WDR77 / Androgen receptor cofactor p44 / Methylosome protein 50 / MEP-50 / 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 frugiperda (fall armyworm) / References: UniProt: Q9BQA1

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Non-polymers , 4 types, 158 molecules

#3: Chemical ChemComp-A1CHO / (1S,2R,3S,5R)-3-{2-[2-amino-6-(2-hydroxyethyl)quinolin-7-yl]ethyl}-5-(7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclopentane-1,2-diol


Mass: 433.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.27 M (NH4)2SO4; 0.05 M MES pH 6.75; 23.0% w/v PEG 3350 PROTEIN SOLUTION : 2 mM DTT, 10 % Glycerol, 10 mM HEPES-NaOH pH 7.5, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.197→109.94 Å / Num. obs: 34528 / % possible obs: 52.6 % / Redundancy: 12.9 % / CC1/2: 0.983 / Rpim(I) all: 0.062 / Rsym value: 0.216 / Net I/σ(I): 7.7
Reflection shellResolution: 2.197→2.541 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1726 / CC1/2: 0.587 / Rpim(I) all: 0.547 / Rsym value: 1.865 / % possible all: 7.5

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Processing

Software
NameVersionClassification
autoPROC1.1.7data reduction
XDSVERSION Jun 30 2023data reduction
autoPROCVersion 1.1.7data scaling
Aimlessdata scaling
REFMAC5.8.0267refinement
XDSVERSION Jun 30 2023data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→109.94 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.885 / SU B: 11.278 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.984 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26621 1691 4.9 %RANDOM
Rwork0.22403 ---
obs0.22612 32837 52.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.156 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0 Å2
2---0.38 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→109.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7335 0 66 149 7550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137509
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176871
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.64510232
X-RAY DIFFRACTIONr_angle_other_deg1.0531.57415806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46422.32388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0715.0171159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2281545
X-RAY DIFFRACTIONr_chiral_restr0.0440.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028540
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021749
X-RAY DIFFRACTIONr_mcbond_other1.3154.6283700
X-RAY DIFFRACTIONr_mcangle_it2.3736.9364621
X-RAY DIFFRACTIONr_mcangle_other2.3736.9384622
X-RAY DIFFRACTIONr_scbond_it0.8574.6283808
X-RAY DIFFRACTIONr_scbond_other0.8574.6283809
X-RAY DIFFRACTIONr_scangle_other1.6136.9175612
X-RAY DIFFRACTIONr_long_range_B_refined3.8451.3377696
X-RAY DIFFRACTIONr_long_range_B_other3.83251.3417688
LS refinement shellResolution: 2.2→2.254 Å
RfactorNum. reflection% reflection
Rfree0.257 1 -
Rwork0.345 9 -
obs--0.21 %

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