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- PDB-8sih: Crystal Structure of PRMT4 with Compound YD1-289 -

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Basic information

Entry
Database: PDB / ID: 8sih
TitleCrystal Structure of PRMT4 with Compound YD1-289
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE/INHIBITOR / PRMT4 / YD1-289 / TRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC / TRANSFERASE-INHIBITOR complex
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 H4K12 methyltransferase activity / histone H4R3 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: 2.35 Å
AuthorsSong, X. / Dong, A. / Deng, Y. / Huang, R. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal Structure of PRMT4 with Compound YD1-289
Authors: Song, X. / Dong, A. / Deng, Y. / Huang, R. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionApr 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6364
Polymers40,9471
Non-polymers6903
Water1,44180
1
A: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2738
Polymers81,8932
Non-polymers1,3806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3550 Å2
ΔGint-61 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.582, 86.582, 136.026
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThis construct only comprises the methyltransferase domain of CARM1 (PRMT4). The authors do not know the quaternary structure of this domain in isolation. However, the software PISA predicts it to be a dimer.

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Components

#1: Protein Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4


Mass: 40946.520 Da / Num. of mol.: 1 / Fragment: methyltransferase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q86X55, type I protein arginine methyltransferase
#2: Chemical ChemComp-I1K / 5'-{[2-(benzylcarbamamido)ethyl][3-(N'-cyclopentylcarbamimidamido)propyl]amino}-5'-deoxyadenosine


Mass: 609.723 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43N11O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.59 Å3/Da / Density % sol: 65.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5 M Ammonium chloride, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 25134 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.02 / Rrim(I) all: 0.057 / Χ2: 0.741 / Net I/σ(I): 10.3 / Num. measured all: 206006
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.35-2.398.20.98712350.7020.9080.3671.0550.666100
2.39-2.438.10.78312260.8250.9510.2910.8360.672100
2.43-2.487.80.64712530.8380.9550.2460.6930.676100
2.48-2.537.10.53712200.8820.9680.2120.5780.69399.7
2.53-2.598.40.45712340.9450.9860.1670.4870.695100
2.59-2.658.80.38312250.9560.9890.1370.4070.69399.9
2.65-2.718.70.2912710.9750.9940.1040.3090.701100
2.71-2.798.80.24512420.9820.9950.0880.2610.726100
2.79-2.878.70.1912230.9880.9970.0680.2020.738100
2.87-2.968.60.15712470.9920.9980.0570.1670.74100
2.96-3.078.50.1112560.9960.9990.040.1170.738100
3.07-3.198.40.08912430.9970.9990.0330.0950.791100
3.19-3.338.20.06712700.9980.9990.0250.0720.805100
3.33-3.517.80.05512340.99810.0210.0590.81699.8
3.51-3.736.90.04512590.99810.0180.0480.82899.8
3.73-4.028.60.0412650.99910.0140.0420.793100
4.02-4.428.40.03712660.99910.0140.0390.84599.6
4.42-5.068.20.03312810.99910.0120.0360.81199.3
5.06-6.378.10.03212910.99910.0120.0340.73100
6.37-507.50.02713930.99910.010.0290.66499.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→45.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.047 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24587 519 2.1 %RANDOM
Rwork0.19613 ---
obs0.19723 24580 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.27 Å20 Å2
2--0.53 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: 1 / Resolution: 2.35→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 46 80 2730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132759
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172455
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.6313756
X-RAY DIFFRACTIONr_angle_other_deg1.2591.5865682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6515338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89222.985134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64915426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9241510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023218
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02612
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6665.6851344
X-RAY DIFFRACTIONr_mcbond_other4.6595.6831342
X-RAY DIFFRACTIONr_mcangle_it6.2898.5121684
X-RAY DIFFRACTIONr_mcangle_other6.2888.5121685
X-RAY DIFFRACTIONr_scbond_it5.6516.161415
X-RAY DIFFRACTIONr_scbond_other5.6526.1591413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8729.052071
X-RAY DIFFRACTIONr_long_range_B_refined9.8365.2222909
X-RAY DIFFRACTIONr_long_range_B_other9.83665.2212900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 27 -
Rwork0.295 1806 -
obs--100 %

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