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- PDB-8uqh: X-ray crystal structure of PRMT4 bound to compound YD-1130 -

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Basic information

Entry
Database: PDB / ID: 8uqh
TitleX-ray crystal structure of PRMT4 bound to compound YD-1130
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE
Function / homology
Function and homology information


negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / histone H3R8 methyltransferase activity ...negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / histone arginine N-methyltransferase activity / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / 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 / positive regulation of epithelial cell apoptotic process / histone H2AQ104 methyltransferase activity / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / response to cAMP / : / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian expression / Activation of gene expression by SREBF (SREBP) / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / : / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / RMTs methylate histone arginines / : / DNA-binding transcription factor binding / methylation / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / : / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBush, M. / Noinaj, N. / Deng, Y. / Huang, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA236356 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA281024 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA26818 United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: An Adenosine Analogue Library Reveals Insights into Active Sites of Protein Arginine Methyltransferases and Enables the Discovery of a Selective PRMT4 Inhibitor.
Authors: Deng, Y. / Kim, E.J. / Song, X. / Kulkarni, A.S. / Zhu, R.X. / Wang, Y. / Bush, M. / Dong, A. / Noinaj, N. / Min, J. / Xu, W. / Huang, R.
History
DepositionOct 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,0788
Polymers155,0974
Non-polymers1,9824
Water19,1501063
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,15616
Polymers310,1938
Non-polymers3,9638
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area23770 Å2
ΔGint-156 kcal/mol
Surface area94030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.726, 98.728, 206.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
Histone-arginine methyltransferase CARM1


Mass: 38774.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1 / Production host: unidentified baculovirus / References: UniProt: Q86X55
#2: Chemical
ChemComp-X9L / 5'-S-(2-{[(3-bromophenyl)methyl]amino}ethyl)-5'-thioadenosine


Mass: 495.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23BrN6O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1063 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 7.5% (w/v) PEG 20,000, 0.1M Tris, 0.08M sodium formate, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.87→74.81 Å / Num. obs: 124972 / % possible obs: 98.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.93 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.08 / Rrim(I) all: 0.208 / Net I/σ(I): 4.9
Reflection shellResolution: 1.87→1.9 Å / Redundancy: 5.73 % / Num. unique obs: 5739 / CC1/2: 0.355 / % possible all: 92.25

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→68.71 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 1999 1.69 %
Rwork0.214 --
obs0.215 118444 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→68.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10748 0 120 1063 11931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.598
X-RAY DIFFRACTIONf_dihedral_angle_d14.9434091
X-RAY DIFFRACTIONf_chiral_restr0.0461690
X-RAY DIFFRACTIONf_plane_restr0.0051968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.3837810.36444689X-RAY DIFFRACTION54
1.92-1.970.34281090.34716381X-RAY DIFFRACTION72
1.97-2.030.37991300.32797592X-RAY DIFFRACTION86
2.03-2.090.36411480.31058601X-RAY DIFFRACTION98
2.09-2.170.34841510.29728749X-RAY DIFFRACTION100
2.17-2.250.31461510.27998820X-RAY DIFFRACTION100
2.25-2.360.30691500.2668801X-RAY DIFFRACTION100
2.36-2.480.32571530.25538854X-RAY DIFFRACTION100
2.48-2.640.29831520.2368841X-RAY DIFFRACTION100
2.64-2.840.27391520.238861X-RAY DIFFRACTION100
2.84-3.120.27491530.22188922X-RAY DIFFRACTION100
3.12-3.580.24661540.18568959X-RAY DIFFRACTION100
3.58-4.510.17311550.15679031X-RAY DIFFRACTION100
4.51-68.710.18961600.16619344X-RAY DIFFRACTION100

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