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- PDB-8g2i: Crystal Structure of PRMT4 with Compound YD1290 -

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Basic information

Entry
Database: PDB / ID: 8g2i
TitleCrystal Structure of PRMT4 with Compound YD1290
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE/INHIBITOR / PRMT4 / YD1290 / 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 / type I protein arginine methyltransferase / negative regulation of dendrite development / 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 / protein-arginine N-methyltransferase activity ...histone H3R17 methyltransferase activity / histone H3R2 methyltransferase activity / type I protein arginine methyltransferase / negative regulation of dendrite development / 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 / protein-arginine N-methyltransferase activity / positive regulation of epithelial cell apoptotic process / positive regulation of transcription by RNA polymerase I / histone methyltransferase activity / 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 / methylation / 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: 2.17 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: Acta Pharm Sin B / Year: 2023
Title: A unique binding pocket induced by a noncanonical SAH mimic to develop potent and selective PRMT inhibitors.
Authors: Deng, Y. / Song, X. / Iyamu, I.D. / Dong, A. / Min, J. / Huang, R.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 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)41,7234
Polymers40,9471
Non-polymers7773
Water86548
1
A: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4478
Polymers81,8932
Non-polymers1,5546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area25040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.659, 86.659, 137.066
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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-I0B / 5'-([2-(benzylcarbamamido)ethyl]{3-[N'-(3-bromophenyl)carbamimidamido]propyl}amino)-5'-deoxyadenosine


Mass: 696.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38BrN11O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M BICINE pH 9.0, 2.0 M Magnesium chloride hexahydrate

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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 EIGER2 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: 2.17→50 Å / Num. obs: 32051 / % possible obs: 99.6 % / Redundancy: 16.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.069 / Χ2: 0.692 / Net I/σ(I): 7.2
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 2 / Num. unique obs: 1557 / CC1/2: 0.851 / CC star: 0.955 / Χ2: 0.558 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→45.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.463 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22466 1521 4.8 %RANDOM
Rwork0.20064 ---
obs0.20177 30483 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.094 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.17→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 48 48 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132726
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172421
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.633711
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5815605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8075335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77523.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01615425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7591510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
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_it4.8014.661329
X-RAY DIFFRACTIONr_mcbond_other4.7714.661327
X-RAY DIFFRACTIONr_mcangle_it6.1186.9641664
X-RAY DIFFRACTIONr_mcangle_other6.1166.9631665
X-RAY DIFFRACTIONr_scbond_it6.4455.1751397
X-RAY DIFFRACTIONr_scbond_other6.4435.1741398
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.7497.5472047
X-RAY DIFFRACTIONr_long_range_B_refined10.39154.0752905
X-RAY DIFFRACTIONr_long_range_B_other10.39654.1012901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.225 Å
RfactorNum. reflection% reflection
Rfree0.358 110 -
Rwork0.288 2190 -
obs--98.84 %

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