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- PDB-6arv: Crystal structure of CARM1 with Compound 2 and SAH -

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Basic information

Entry
Database: PDB / ID: 6arv
TitleCrystal structure of CARM1 with Compound 2 and SAH
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / protein-inhibitor complex / protein arginine methyltransferase
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) / 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-BW7 / S-ADENOSYL-L-HOMOCYSTEINE / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBoriack-Sjodin, P.A. / Jin, L.
CitationJournal: Sci Rep / Year: 2017
Title: Identification of a CARM1 Inhibitor with Potent In Vitro and In Vivo Activity in Preclinical Models of Multiple Myeloma.
Authors: Drew, A.E. / Moradei, O. / Jacques, S.L. / Rioux, N. / Boriack-Sjodin, A.P. / Allain, C. / Scott, M.P. / Jin, L. / Raimondi, A. / Handler, J.L. / Ott, H.M. / Kruger, R.G. / McCabe, M.T. / ...Authors: Drew, A.E. / Moradei, O. / Jacques, S.L. / Rioux, N. / Boriack-Sjodin, A.P. / Allain, C. / Scott, M.P. / Jin, L. / Raimondi, A. / Handler, J.L. / Ott, H.M. / Kruger, R.G. / McCabe, M.T. / Sneeringer, C. / Riera, T. / Shapiro, G. / Waters, N.J. / Mitchell, L.H. / Duncan, K.W. / Moyer, M.P. / Copeland, R.A. / Smith, J. / Chesworth, R. / Ribich, S.A.
History
DepositionAug 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)162,68923
Polymers158,4924
Non-polymers4,19719
Water13,025723
1
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,39112
Polymers79,2462
Non-polymers2,14410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-30 kcal/mol
Surface area26720 Å2
MethodPISA
2
C: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,29911
Polymers79,2462
Non-polymers2,0529
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-27 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.230, 99.120, 208.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 39623.121 Da / Num. of mol.: 4 / Fragment: Catalytic domain (UNP residues 134-479)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Plasmid: pFastbac / Cell line (production host): Sf9
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q86X55, type I protein arginine methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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-BW7 / (2R)-1-amino-3-{3-[4-(morpholin-4-yl)-1-(propan-2-yl)-1H-pyrazolo[3,4-b]pyridin-6-yl]phenoxy}propan-2-ol


Mass: 411.497 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H29N5O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 723 / 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: 2.48 Å3/Da / Density % sol: 50.47 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→70.78 Å / Num. obs: 105501 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.097 / Rsym value: 0.086 / Net I/av σ(I): 6.8 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2-2.054.40.7610.977360.4170.8710.76199.9
2.05-2.114.50.6131.175860.3350.7020.61399.8
2.11-2.174.50.4891.473470.2660.5590.48999.8
2.17-2.244.60.3941.871070.2130.450.39499.7
2.24-2.314.60.3182.269340.1710.3620.31899.7
2.31-2.394.70.2672.666800.1430.3040.26799.7
2.39-2.484.80.2283.164930.1210.2590.22899.6
2.48-2.584.90.1853.862130.0970.2110.18599.6
2.58-2.74.90.1544.659720.080.1740.15499.4
2.7-2.834.90.1255.657180.0650.1410.12599.3
2.83-2.984.90.1056.753950.0540.1190.10599.2
2.98-3.164.90.0877.951540.0450.0990.08799
3.16-3.384.80.0719.348120.0370.0810.07199.1
3.38-3.654.70.06110.445180.0310.0690.06199.1
3.65-44.70.05311.542070.0280.060.05399.4
4-4.474.90.04712.937850.0240.0520.04799.2
4.47-5.164.80.04214.533730.0210.0470.04299.3
5.16-6.324.90.0414.829030.020.0450.0499.5
6.32-8.944.70.03514.622830.0180.0390.03599.6
8.94-70.7784.10.03114.812850.0170.0360.03196.7

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→70.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.461 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.165
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5266 5 %RANDOM
Rwork0.1891 ---
obs0.1913 100150 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.18 Å2 / Biso mean: 30.185 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--1.17 Å20 Å2
3----0.9 Å2
Refinement stepCycle: final / Resolution: 2→70.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11048 0 290 723 12061
Biso mean--33.84 36.15 -
Num. residues----1376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211777
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.96915978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8551412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26123.975551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.005151943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2381557
X-RAY DIFFRACTIONr_chiral_restr0.0890.21741
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218942
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 402 -
Rwork0.261 6914 -
all-7316 -
obs--99.85 %

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