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- PDB-5u4x: Coactivator-associated arginine methyltransferase 1 with TP-064 -

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Basic information

Entry
Database: PDB / ID: 5u4x
TitleCoactivator-associated arginine methyltransferase 1 with TP-064
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / CARM1 / methyltransferase / TP-064 / Structural Genomics / Structural Genomics Consortium / SGC
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 / protein-arginine N-methyltransferase activity / replication fork reversal ...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 / protein-arginine N-methyltransferase activity / replication fork reversal / 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 / Heme signaling / lysine-acetylated histone binding / 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 / methylation / 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 / cytoplasm / cytosol
Similarity search - Function
Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily ...Histone-arginine methyltransferase CARM1, N-terminal / Coactivator-associated arginine methyltransferase 1 N terminal / Ribosomal protein L11 methyltransferase (PrmA) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Vaccinia Virus protein VP39 / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-7VM / S-ADENOSYL-L-HOMOCYSTEINE / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsDONG, A. / ZENG, H. / Saikatendu, K.S. / STONE, H. / WALKER, J.R. / Seitova, A. / Hutchinson, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...DONG, A. / ZENG, H. / Saikatendu, K.S. / STONE, H. / WALKER, J.R. / Seitova, A. / Hutchinson, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: Oncotarget / Year: 2018
Title: TP-064, a potent and selective small molecule inhibitor of PRMT4 for multiple myeloma.
Authors: Nakayama, K. / Szewczyk, M.M. / Dela Sena, C. / Wu, H. / Dong, A. / Zeng, H. / Li, F. / de Freitas, R.F. / Eram, M.S. / Schapira, M. / Baba, Y. / Kunitomo, M. / Cary, D.R. / Tawada, M. / ...Authors: Nakayama, K. / Szewczyk, M.M. / Dela Sena, C. / Wu, H. / Dong, A. / Zeng, H. / Li, F. / de Freitas, R.F. / Eram, M.S. / Schapira, M. / Baba, Y. / Kunitomo, M. / Cary, D.R. / Tawada, M. / Ohashi, A. / Imaeda, Y. / Saikatendu, K.S. / Grimshaw, C.E. / Vedadi, M. / Arrowsmith, C.H. / Barsyte-Lovejoy, D. / Kiba, A. / Tomita, D. / Brown, P.J.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / struct / Item: _struct.title
Revision 1.2May 23, 2018Group: Data collection / 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
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)158,35730
Polymers154,9854
Non-polymers3,37226
Water12,376687
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,17813
Polymers77,4922
Non-polymers1,68611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-22 kcal/mol
Surface area25350 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,17817
Polymers77,4922
Non-polymers1,68615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-22 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.091, 98.919, 207.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-506-

UNX

21C-778-

HOH

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Components

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


Mass: 38746.148 Da / Num. of mol.: 4 / Fragment: UNP residues 140-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q86X55, type I protein arginine methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-7VM / N-methyl-N-[(2-{1-[2-(methylamino)ethyl]piperidin-4-yl}pyridin-4-yl)methyl]-3-phenoxybenzamide


Mass: 458.595 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H34N4O2
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 18 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% PEG 3350, 0.2 M AmSO4, 0.1 M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 126636 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.034 / Rrim(I) all: 0.096 / Χ2: 0.844 / Net I/σ(I): 6.2 / Num. measured all: 971179
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
1.88-1.917.31.02162500.751100
1.91-1.957.60.6780.7821100
1.95-1.987.60.7850.8621100
1.98-2.037.60.6230.8911100
2.03-2.077.70.5030.9171100
2.07-2.127.70.4420.9481100
2.12-2.177.70.4070.9541100
2.17-2.237.70.3530.9671100
2.23-2.297.70.2330.9741100
2.29-2.377.70.2670.9811100
2.37-2.457.70.2170.9851100
2.45-2.557.80.1910.9891100
2.55-2.677.80.1570.9921100
2.67-2.817.80.1240.9941100
2.81-2.987.80.1030.9961100
2.98-3.217.80.0770.9981100
3.21-3.547.80.060.9981100
3.54-4.057.80.0480.9991100
4.05-5.17.80.0380.9991100
5.1-507.30.040.999198.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IKP

4ikp


Resolution: 1.88→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.151 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.126
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 2521 2 %RANDOM
Rwork0.1878 ---
obs0.1884 123618 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.09 Å2 / Biso mean: 28.661 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å2-0 Å2
2---0.03 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10502 0 258 700 11460
Biso mean--24.66 34.59 -
Num. residues----1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911368
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210557
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.94615485
X-RAY DIFFRACTIONr_angle_other_deg0.916324262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30851399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08824.186516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.907151827
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2271547
X-RAY DIFFRACTIONr_chiral_restr0.0830.21687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213421
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022792
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 177 -
Rwork0.255 9038 -
all-9215 -
obs--99.99 %

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