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- PDB-8sig: Crystal Structure of PRMT4 with Compound YD1-288 -

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Basic information

Entry
Database: PDB / ID: 8sig
TitleCrystal Structure of PRMT4 with Compound YD1-288
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE/INHIBITOR / PRMT4 / YD1-288 / TRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium / SGC / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal ...: / histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / negative regulation of dendrite development / type I protein arginine methyltransferase / protein-arginine omega-N asymmetric methyltransferase activity / protein methyltransferase activity / histone arginine N-methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / positive regulation of fat cell differentiation / response to cAMP / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / lysine-acetylated histone binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / RMTs methylate histone arginines / Transcriptional regulation of white adipocyte differentiation / Circadian Clock / DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription coactivator activity / transcription cis-regulatory region binding / 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) / 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: 1.78 Å
AuthorsSong, X. / Dong, A. / Deng, Y. / Huang, R. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: Crystal Structure of PRMT4 with Compound YD1-288
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)41,46910
Polymers40,9471
Non-polymers5239
Water4,468248
1
A: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,93820
Polymers81,8932
Non-polymers1,04518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3650 Å2
ΔGint-38 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.887, 84.887, 130.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-820-

HOH

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-GWU / 5'-{(3-aminopropyl)[2-(benzylcarbamamido)ethyl]amino}-5'-deoxyadenosine


Mass: 499.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H33N9O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Calcium chloride dihydrate, 0.1 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400

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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: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 53004 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.025 / Rrim(I) all: 0.082 / Χ2: 1.18 / Net I/σ(I): 7.6 / Num. measured all: 553802
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
1.78-1.8110.50.99226330.7770.9350.3211.0430.591
1.81-1.8410.40.80826280.8420.9560.2620.850.604
1.84-1.8810.20.69326010.8870.970.2280.730.635
1.88-1.929.50.5525850.9040.9740.1870.5820.67
1.92-1.969.40.44926190.9310.9820.1540.4750.714
1.96-2110.3726380.9650.9910.1170.3890.752
2-2.0511.10.31326190.9740.9930.0980.3280.795
2.05-2.1111.10.25626230.9810.9950.080.2690.849
2.11-2.17110.21426240.9850.9960.0680.2250.927
2.17-2.2410.90.18226200.9890.9970.0580.1910.953
2.24-2.3210.80.15726170.9920.9980.050.1651.043
2.32-2.4210.70.13426580.9930.9980.0430.1411.101
2.42-2.5310.50.11826440.9940.9990.0380.1241.165
2.53-2.66100.10126330.9960.9990.0340.1071.352
2.66-2.839.30.08726700.9960.9990.030.0921.485
2.83-3.0411.10.07726470.9970.9990.0240.0811.634
3.04-3.3511.10.06826790.9980.9990.0220.0722.029
3.35-3.8310.80.05826910.99810.0180.0612.291
3.83-4.8310.10.0527040.99810.0170.0532.323
4.83-509.80.03828710.99910.0130.041.524

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→48.91 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.259 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19928 1035 2 %RANDOM
Rwork0.18335 ---
obs0.18369 51923 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.78→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 44 248 2920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132904
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172598
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.6343966
X-RAY DIFFRACTIONr_angle_other_deg1.3291.5816025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06222.568148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8715465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3271515
X-RAY DIFFRACTIONr_chiral_restr0.0680.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023437
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02655
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_it2.1432.7961415
X-RAY DIFFRACTIONr_mcbond_other2.1372.7931413
X-RAY DIFFRACTIONr_mcangle_it3.0574.1831792
X-RAY DIFFRACTIONr_mcangle_other3.0564.1821793
X-RAY DIFFRACTIONr_scbond_it2.7913.0641489
X-RAY DIFFRACTIONr_scbond_other2.7923.0641487
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2444.4912172
X-RAY DIFFRACTIONr_long_range_B_refined6.12133.8063258
X-RAY DIFFRACTIONr_long_range_B_other6.00333.3553198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.825 Å
RfactorNum. reflection% reflection
Rfree0.306 73 -
Rwork0.282 3782 -
obs--99.18 %

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