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- PDB-6dvr: Crystal structure of human CARM1 with (R)-SKI-72 -

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Basic information

Entry
Database: PDB / ID: 6dvr
TitleCrystal structure of human CARM1 with (R)-SKI-72
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CARM1 / PRMT4 / SKI-72 inhibitor / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-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) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / Distorted Sandwich / PH-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-HDG / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsDong, A. / Zeng, H. / Hutchinson, A. / Seitova, A. / Luo, M. / Cai, X.C. / Ke, W. / Wang, J. / Shi, C. / Zheng, W. ...Dong, A. / Zeng, H. / Hutchinson, A. / Seitova, A. / Luo, M. / Cai, X.C. / Ke, W. / Wang, J. / Shi, C. / Zheng, W. / Lee, J.P. / Ibanez, G. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of human CARM1 with (R)-SKI-72
Authors: Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Luo, M. / Cai, X.C. / Ke, W. / Wang, J. / Shi, C. / Zheng, W. / Lee, J.P. / Ibanez, G. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Zeng, H. / Dong, A. / Hutchinson, A. / Seitova, A. / Luo, M. / Cai, X.C. / Ke, W. / Wang, J. / Shi, C. / Zheng, W. / Lee, J.P. / Ibanez, G. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Structural Genomics Consortium (SGC)
History
DepositionJun 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,78312
Polymers77,9532
Non-polymers1,83010
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-22 kcal/mol
Surface area25720 Å2
2
A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules

A: Histone-arginine methyltransferase CARM1
B: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,13248
Polymers311,8128
Non-polymers7,32140
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area24340 Å2
ΔGint-148 kcal/mol
Surface area91940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.366, 98.579, 207.375
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 38976.453 Da / Num. of mol.: 2
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-HDG / (2R,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-[(benzylamino)methyl]-N-[2-(4-methoxyphenyl)ethyl]hexanamide (non-preferred name) / (R)-SKI-72


Mass: 618.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H42N8O5
#3: Chemical ChemComp-P15 / 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL


Mass: 296.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H28O7
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.44 Å3/Da / Density % sol: 49.54 % / Mosaicity: 0.301 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3350, 0.2 M NH4SO4, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 112857 / % possible obs: 100 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.016 / Rrim(I) all: 0.052 / Χ2: 0.624 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.54-1.5710.40.97755730.780.3161.0280.428100
1.57-1.610.90.79855660.8390.2520.8380.427100
1.6-1.6310.80.67955940.870.2150.7130.424100
1.63-1.6610.80.55655750.9150.1770.5840.429100
1.66-1.6910.70.48156250.9350.1530.5050.44100
1.69-1.7310.60.39256020.9540.1260.4120.437100
1.73-1.7810.10.3156000.9690.1020.3270.446100
1.78-1.839.20.25356180.9790.0870.2680.457100
1.83-1.8810.80.19855740.9890.0630.2080.472100
1.88-1.9411.30.15656090.9930.0480.1640.527100
1.94-2.0111.20.11956480.9960.0370.1250.519100
2.01-2.09110.09556050.9970.030.10.566100
2.09-2.1910.70.07956430.9980.0250.0830.588100
2.19-2.39.80.06656260.9980.0220.070.66899.9
2.3-2.4410.90.05656430.9990.0180.0590.703100
2.44-2.6311.40.0556750.9990.0150.0530.76100
2.63-2.911.20.04456690.9990.0130.0460.87100
2.9-3.32100.03757010.9990.0120.0391.02599.9
3.32-4.1811.10.032576610.010.0341.23499.9
4.18-5010.50.02859450.9990.0090.0290.98199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IKP

4ikp


Resolution: 1.54→44.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.572 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.078
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1658 1.5 %RANDOM
Rwork0.1946 ---
obs0.1949 110906 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.9 Å2 / Biso mean: 23.388 Å2 / Biso min: 12.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0 Å2
2--0.22 Å20 Å2
3----0.6 Å2
Refinement stepCycle: final / Resolution: 1.54→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5275 0 129 413 5817
Biso mean--29.91 34.12 -
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0155807
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175114
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.7347915
X-RAY DIFFRACTIONr_angle_other_deg0.4251.72811959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16320.558215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90415824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.851524
X-RAY DIFFRACTIONr_chiral_restr0.0530.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216843
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021189
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 122 -
Rwork0.268 8095 -
all-8217 -
obs--99.96 %

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