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- PDB-8g2h: Crystal Structure of PRMT4 with Compound YD1113 -

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Basic information

Entry
Database: PDB / ID: 8g2h
TitleCrystal Structure of PRMT4 with Compound YD1113
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE/INHIBITOR / PRMT4 / YD1113 / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


histone H3R17 methyltransferase activity / negative regulation of dendrite development / histone H3R2 methyltransferase activity / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / : / protein methyltransferase activity / regulation of intracellular estrogen receptor signaling pathway / replication fork reversal / protein-arginine N-methyltransferase activity ...histone H3R17 methyltransferase activity / negative regulation of dendrite development / histone H3R2 methyltransferase activity / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase / : / 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 / histone methyltransferase activity / positive regulation of transcription by RNA polymerase I / nuclear replication fork / response to cAMP / positive regulation of fat cell differentiation / : / 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 / : / methylation / DNA-binding transcription factor binding / 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 / cytoplasm / cytosol
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
Chem-YVU / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)41,61310
Polymers40,9471
Non-polymers6679
Water3,333185
1
A: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,22620
Polymers81,8932
Non-polymers1,33318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4600 Å2
ΔGint-45 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.215, 84.215, 130.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 194 molecules

#2: Chemical ChemComp-YVU / 5'-S-[2-(benzylcarbamamido)ethyl]-5'-thioadenosine


Mass: 459.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium chloride dihydrate, 0.05 M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400, 0.002 M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 87534 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.065 / Χ2: 1.135 / Net I/σ(I): 12.6
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.945 / Mean I/σ(I) obs: 2 / Num. unique obs: 4297 / CC1/2: 0.75 / CC star: 0.926 / Χ2: 0.706 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0258refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→48.66 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.962 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17745 1683 1.9 %RANDOM
Rwork0.17134 ---
obs0.17147 85796 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.49→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 50 185 2887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172617
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6313987
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5816079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3315363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59722.993147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.68315471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7231512
X-RAY DIFFRACTIONr_chiral_restr0.0790.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023448
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02648
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_it1.3911.8821412
X-RAY DIFFRACTIONr_mcbond_other1.3911.8841412
X-RAY DIFFRACTIONr_mcangle_it2.0642.8191789
X-RAY DIFFRACTIONr_mcangle_other2.0632.8191790
X-RAY DIFFRACTIONr_scbond_it2.412.21510
X-RAY DIFFRACTIONr_scbond_other2.4092.2011511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.713.1942199
X-RAY DIFFRACTIONr_long_range_B_refined5.25523.3353241
X-RAY DIFFRACTIONr_long_range_B_other4.91422.9993189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.491→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 109 -
Rwork0.266 6109 -
obs--96.6 %

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