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- PDB-6s7c: Crystal structure of CARM1 in complex with inhibitor UM079 -

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Basic information

Entry
Database: PDB / ID: 6s7c
TitleCrystal structure of CARM1 in complex with inhibitor UM079
ComponentsHistone-arginine methyltransferase CARM1
KeywordsTRANSFERASE / Inhibitor / Complex / Arginine methyltransferase
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) / Hnrnp arginine n-methyltransferase1 / Hnrnp arginine n-methyltransferase1 / Arginine methyltransferase oligomerization subdomain / Protein arginine N-methyltransferase / SAM-dependent methyltransferase PRMT-type domain profile. / 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 / Arginine methyltransferase oligomerization subdomain / 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-KY2 / Histone-arginine methyltransferase CARM1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGunnell, E.A. / Muhsen, U. / Dowden, J. / Dreveny, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)1501569 United Kingdom
CitationJournal: Biochem.J. / Year: 2020
Title: Structural and biochemical evaluation of bisubstrate inhibitors of protein arginine N-methyltransferases PRMT1 and CARM1 (PRMT4).
Authors: Gunnell, E.A. / Al-Noori, A. / Muhsen, U. / Davies, C.C. / Dowden, J. / Dreveny, I.
History
DepositionJul 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 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)161,7848
Polymers160,0944
Non-polymers1,6904
Water3,153175
1
A: Histone-arginine methyltransferase CARM1
C: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8924
Polymers80,0472
Non-polymers8452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-24 kcal/mol
Surface area25900 Å2
MethodPISA
2
B: Histone-arginine methyltransferase CARM1
D: Histone-arginine methyltransferase CARM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8924
Polymers80,0472
Non-polymers8452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-24 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.697, 98.629, 207.438
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: 40023.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARM1, PRMT4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q86X55, type I protein arginine methyltransferase
#2: Chemical
ChemComp-KY2 / 1-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azanylpropyl)amino]propyl]guanidine


Mass: 422.485 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H30N10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-tris propane, 0.02 M sodium phosphate, 21 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→56.62 Å / Num. obs: 66343 / % possible obs: 96.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 40.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.041 / Rrim(I) all: 0.086 / Net I/σ(I): 11.8 / Num. measured all: 279649 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.354.20.74144770.6840.4120.85598.2
10.79-56.6240.0347170.9980.0190.03993.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→51.86 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.97
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 3320 5.01 %RANDOM
Rwork0.2058 ---
obs0.2072 66203 95.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.52 Å2 / Biso mean: 46.6834 Å2 / Biso min: 22.64 Å2
Refinement stepCycle: final / Resolution: 2.3→51.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10976 0 120 175 11271
Biso mean--58.53 40.99 -
Num. residues----1368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.33290.34121210.32652676279798
2.3329-2.36770.32251290.30742626275598
2.3677-2.40470.31821220.30492665278798
2.4047-2.44410.26821340.29172656279099
2.4441-2.48630.28051340.28862643277798
2.4863-2.53150.29751390.27252613275297
2.5315-2.58020.28811440.26532665280998
2.5802-2.63280.29721240.25982598272296
2.6328-2.69010.30341380.24942573271195
2.6901-2.75260.25281560.24822520267694
2.7526-2.82150.28031430.23722606274998
2.8215-2.89780.28011300.23922659278998
2.8978-2.9830.28431480.22652671281998
2.983-3.07930.23391090.21552646275597
3.0793-3.18930.25611470.22342632277997
3.1893-3.3170.25741400.21052616275696
3.317-3.46790.24741320.20662577270995
3.4679-3.65070.24081450.19552549269492
3.6507-3.87940.2121540.18732634278897
3.8794-4.17880.20611550.17462634278996
4.1788-4.59910.19231460.1632630277695
4.5991-5.2640.20071370.15482511264890
5.264-6.630.21131400.18592646278694
6.63-51.87270.16771530.16942637279089
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.43810.4192-0.32682.10750.17931.7266-0.06030.2639-0.2565-0.15040.01220.14730.0658-0.03740.17670.30180.0716-0.03040.3521-0.06730.260216.5114107.067371.4946
20.9253-0.5323-0.36241.1450.15430.62930.00690.02370.07570.04-0.0046-0.18090.02150.2263-0.04740.14920.0239-0.04280.30030.00350.218619.2529127.967385.7807
31.5346-0.5153-0.43132.9576-0.16181.1006-0.0132-0.11620.07810.145-0.02-0.0441-0.17730.1154-0.01450.22990.0586-0.05050.3017-0.0040.233416.685129.220393.3512
42.0995-0.55110.28241.2222-0.32331.6111-0.0604-0.2688-0.20370.05390.0362-00.1359-0.01780.0870.4569-0.0944-0.03280.52840.05250.3013-14.0291106.169932.22
50.73960.3635-0.05950.7891-0.30130.3930.0932-0.09140.0552-0.0169-0.06610.1390.0672-0.2463-0.05820.3437-0.0504-0.0390.4524-0.04560.2399-18.0325126.723717.9902
61.8616-0.29590.00982.3227-0.72770.80290.1145-0.05830.0612-0.0666-0.1380.0446-0.0405-0.2412-0.01970.4154-0.0546-0.06280.5017-0.07460.2568-15.8739128.16910.0784
71.27410.40480.40681.30360.11962.47580.202-0.0903-0.1524-0.15880.04070.05140.3135-0.1153-0.08410.2451-0.0957-0.07680.28750.05160.2952-16.971129.784493.29
80.1351-0.1316-0.30540.5250.0951.99120.2869-0.0329-0.0093-0.0486-0.14860.12950.0957-0.05540.01270.3825-0.1245-0.12980.37710.06610.3648-23.8609123.944882.1934
90.6137-0.4167-0.51480.47160.71561.17840.29260.5122-0.0166-0.5148-0.14840.02670.08570.169-0.260.47840.0492-0.13050.5247-0.00650.3364.2832117.441258.1719
101.79440.1616-0.91861.10050.54472.6580.17850.2443-0.1833-0.0874-0.15230.1032-0.1075-0.2604-0.05960.3861-0.0321-0.1780.41240.08380.3654-20.7521124.908270.8178
111.1535-0.0703-0.21420.80820.55792.21290.14890.3155-0.0194-0.1963-0.0408-0.0292-0.0078-0.1956-0.04990.3433-0.0018-0.10920.41810.08780.3014-20.3656128.264366.2562
120.89070.0405-1.19560.90230.15331.15510.20520.1557-0.01780.0445-0.1224-0.12660.2998-0.0053-0.05690.4332-0.0078-0.12170.43720.01540.375-14.5378117.15766.2087
131.0027-0.44010.55211.3585-0.28871.99280.103-0.01-0.04960.0159-0.0148-0.00890.18520.08770.00540.39480.0684-0.040.4361-0.03480.238318.7913130.130410.8099
140.75180.4110.26050.2182-0.33970.60220.0965-0.28280.00430.1094-0.0668-0.0115-0.0143-0.1035-0.06560.46720.0698-0.05660.5442-0.07710.31367.9052121.336538.5894
150.8725-0.2514-0.61960.6965-1.03861.74350.1054-0.30320.00570.1413-0.1550.049-0.29310.25650.03160.4336-0.013-0.09180.576-0.06850.26821.6804128.488935.8413
160.93730.2717-0.35550.54740.04352.59550.061-0.1682-0.0244-0.151-0.08820.020.0531-0.16670.02160.40290.0086-0.08720.5129-0.01750.291316.4703118.265937.4888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 135 through 252 )A135 - 252
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 432 )A253 - 432
3X-RAY DIFFRACTION3chain 'A' and (resid 433 through 476 )A433 - 476
4X-RAY DIFFRACTION4chain 'B' and (resid 135 through 252 )B135 - 252
5X-RAY DIFFRACTION5chain 'B' and (resid 253 through 432 )B253 - 432
6X-RAY DIFFRACTION6chain 'B' and (resid 433 through 476 )B433 - 476
7X-RAY DIFFRACTION7chain 'C' and (resid 135 through 264 )C135 - 264
8X-RAY DIFFRACTION8chain 'C' and (resid 265 through 299 )C265 - 299
9X-RAY DIFFRACTION9chain 'C' and (resid 300 through 335 )C300 - 335
10X-RAY DIFFRACTION10chain 'C' and (resid 336 through 368 )C336 - 368
11X-RAY DIFFRACTION11chain 'C' and (resid 369 through 432 )C369 - 432
12X-RAY DIFFRACTION12chain 'C' and (resid 433 through 476 )C433 - 476
13X-RAY DIFFRACTION13chain 'D' and (resid 135 through 278 )D135 - 278
14X-RAY DIFFRACTION14chain 'D' and (resid 279 through 335 )D279 - 335
15X-RAY DIFFRACTION15chain 'D' and (resid 336 through 432 )D336 - 432
16X-RAY DIFFRACTION16chain 'D' and (resid 433 through 476 )D433 - 476

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